I don't feel that is wrong to have the child sleep on the trundle. It sounds as though both boys get along well and I would leave things just as they are in the house.
One thing I do suggest is set boundaries with the ex. You have alot of years to deal with her.
Yes set boundaries now!!! We have one that we never thought we would have to set and that is that she is not to call past 9 pm!! the reason is b/c almost EVERY night she would call around 10ish knowing we were in bed and a lot of times it was OUR time.
