Possibly the pastor came to the back door? This might explain the fact that he was also attacked with a log if they had the woodpile back there.
If he was trying to cover up the murder he would need to dispose of both the bodies and the murder weapons as well as any clothes that would have DNA evidence on them. If he was going to create a story involving a false intruder, however ineptly, he might leave the bodies where they were but still want to dispose of the weapons and clothes somewhere out there.
And I have a feeling deodorant wasn't on his packing list.
Peace gurl may be able to add more, but from the images I've seen it appears that the "garage" portion of the house isn't in fact a garage. It may have been originally, but it looks more like a "mother in law" apartment or one added for a student occupant. Small college towns often have apartments added on to houses near the schools.
The Google aerial view doesn't show a driveway leading to the back side, there is obviously no garage door on the front, and there are bushes and a smaller door on the side away from the main house and towards the drive way. There is a relatively narrow section of the house that connects the main house and the smaller house. The door on the driveway side of the little house is on axis with the connecting section. My guess is that for the occupants, that is the main entry.
There is another door on the front and quite possibly the back of the connector. There seems to be a patio in the back area defined by those three section of house. The front door on the connector is probably mostly unused. The back door if there is one may be the occupant's main entrance, but I would guess not. I would say the most likely is the end door, followed in likelihood by a door on the back left (viewed from the front) corner of the main house. My guess is that is where the kitchen would be and that's a common place for people to enter their own homes. It's also a nearly straight shot from the drive way and there looks to be a walkway that would allow that.
The front door is a formality. Strangers knock and/or enter at the front. Family has its entry, and friends may either enter there accompanied, or may use another door if they come unannounced or if the family entry is into a semi-private zone like a kitchen. Depends on the family, how many doors there are etc.
If the bodies were found upstair in the smaller portion of the house, then there must be an upstairs. It has to be small though. Very small. The roof ridge on it is considerably lower than on the main house. At most about 1/3 of the floor space would be tall enough to stand up in. If you look at the front view of the house, it's pretty easy to see why. If the interior height of the top of the front window were 7 feet, that would leave about 5 feet of width for a 6' tall person to stand in. The slope is about 45 degrees, so a shorter person would only gain in width twice the difference between his height and 6' before hitting his head. There are no dormers. It's pretty tiny up there, and it has to have some sort of access, stairs? spiral staircase maybe, but expensive and a code problem. I cant figure out where they would be considering the roof structure and the chimney, but right to the left after entering the end door makes the most sense. That allows for an entry/mud room before the passage into the main house with enough space for a roughly 15' x 15' room to the back side.
I had considered the possibility that Emma may have claimed the little house as her own. I looked for pictures that might be of her at home with windows or ceiling behind her, but couldn't find any clues there. If she had the upstairs room, which size seems to me to make unlikely anyway, that background would be easy to spot. Downstairs could be hers except for one thing. The main house has a basement. The rest probably doesn't. Connecting the rest to a likely forced air heating/cooling system would be a hassle. It could go through the attic spaces, but that would still be pain with long duct lengths and a hugely increased furnace size. Where does all of that rambling lead? To a conclusion that the smaller section of the house is heated by wood and it has either a 1.3 story guest room, or a guest loft. Emma and Mel may have stayed there if they were alone, but they had Sam, who had to stay somewhere. There's no way he would get her room with or without her, especially if things weren't going well. Maybe all three would have hung out together there though and possibly even all slept there although I doubt it.
I had considered that the girls slept in the loft, Sam got angry, killed them with the maul that would have been nearby, killed the mother with the same implement, and then dragged her there. I think that was his place though and he dragged them all there for some reason, possibly to hide them, possibly to do something else with them. He may have expected to load them in the van and dump them but not found the keys.
I suspect Mr. Niederbrock(seen that spelled both ei and ie) arrived unexpectedly and either came in on his own (how estranged the parents were we don't really know) or knocked at the end door by the driveway. There's a chimney that indicates a fireplace very close to that door. Sam either saw him coming and ambushed him or let him in and caught him off guard. He was probably too heavy for Sam to carry upstairs, which would explain why he was in a different location. The problem I've created though is why the women's bodies were found first. My guess is that the smell from them was much more powerful and that's what police investigating that found. Could have been a trail of blood in at least part of the house.
The relationship between police and people in their own homes is a formal relationship, not a friendly relationship. That demands a knock at the front door, not a side door in most circumstances. I think that's what kept them from seeing or smelling the bodies. Someone asked earlier about the police asking for ID or recognizing someone as not being right there. Police are almost certainly local. College professors and students are almost certainly not. That can be like oil and water even in a very small town. It does affect how people interact.
To add to the list of what Sam knows, if Mels mom called at 3:30 a.m. and he said they were broken down (reported by peace gurl, but both news to me, source?) then he knows he has some explaining to do about why their car is still in the driveway. Same for the pastor's car. He really screwed things up by showing up when he did. i don't think Sam was waiting for him to add to his kill list. I think he had to do it or he would have certainly been caught very soon.
I keep wondering why that house didn't burn down. If I were sitting there trying to come up with a plan, it would have happened sometime Thursday night.