This plays right along with the question alluding to tonneau covers and those of you who have a toolbox in the bed of your truck, you may need to work around it. With tents that do not have a sewn-in bottom, it is possible that you could leave it in your truck. If the toolbox sits flush in your bed and not on the rails, then you are probably in the clear. But, things start to get a little more complicated for the versions that have a sewn-in floor.
Honestly, for ones with a floor, the simplest solution would be to remove the toolbox. If you are content with it being there, you might be able to make a smaller tent work. But, truthfully, if you want your toolbox inside then you should invest in one that does not have a sewn-in floor. It would be significantly easier for you to do it this way, as the tent can sit right over the top of it (if it sits on your bed).