Your question was why move the bodies?
There are two schools of thought on this one. One school of thought is that, since Chris' brother, Ryan, while searching for the little boys, had mentioned to the killer that the little boys might be playing in the manholes (although he didn't mention this to LE at that time), the killer, hearing this mentioned, felt the need to move the bodies, afraid that Ryan might mention it to LE. The killer spent the evening of May 5th in and out of the woods, according to his own statement, but never reported seeing/hearing the commotion Jessie described. IMO, he was "keeping watch" on the bodies because he wanted to move them later, either because he was afraid of evidence left in the manhole that could link to him or because he was afraid that the bodies would be discovered quickly.
The other school of thought, and very few people see this as a possibility, is that the killer wanted the bodies found and was surprised that LE had not found them on the night of the 5th. One of his actions after the murders is the genesis of this line of thought. About two weeks after the murders, he left his wife (temporarily) because she just couldn't "get over" the death of her son. If the bodies were not found quickly, his wife would not be able to accept her son's death. Since he simply couldn't accept his wife's natural grieving process, it stands to reason that he wouldn't accept the natural continued search for the boys if their bodies had not been found. Therefore, the killer wanted the bodies found quickly and moved them to a location where he thought that they would be found more quickly.
Although the second possibility is intriguing, I am more prone to accept the first possibility. Personally, I believe that they were killed in the manhole and that the killer was afraid that he had left some evidence there. Additionally, although some water would be in the bottom of the manhole, the killer might not have believed it to be enough the wash away evidence as he believed that the water in the ditch might have done.
When were the bodies moved? IMO, in all probability, the bodies were moved between 3 am and 5 am on the 6th of May. Most of the searching had stopped by around 3 am, and, as soon as he was sure that everyone was at home in bed and in an exhausted sleep, he returned to the manhole, pulled the bodies out, hogtied them and transported them the short distance to the ditch.