Tie fighter Problems 2

So the model progresses. I selected 5 x 5 grid of vertices at the side and with careful manipulation and extrusion I elongated these into the wing spokes. I also created the guns out of a many segmented cylinder. When it came to boolean these I had problems.

It created extra edges that were warping the model. After trying to delete/add extras. Though I found that the first boolean creates a ring of edges where the 2 elements meet, by copying the gun, deleteing the origional and then boolean them together again, they attached nicely.
I am wondering if attaching at this stage is a good idea. Yes I get a crisp model, but when it comes to UV wrapping it may be troublesome. I think from now on I wont attach till later.