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.

I said what I would do for my child, or what I would do for a stepchild if I had one given my life experiences. I think that all that is needed is the usual minimum space that most people usually have, their own bed, dresser and hopefully a desk so they can keep stuff there and have their own downtime space to go to. I wouldn't treat my dh's child as I would a friend that comes and stays the night but obviously lots of people choose to do so and that's what works for them.