Hello, sideliner, I think, the guns should be rigged first. You will have more room to work in. And, yes, I would be suggesting to 'pin' guns to the deck. However, if you are careful enough to glue the trucks without the use of excessive glue then, you can try. Personally, I use a slightly different method, one end of the brass pin inserted into the front axletree (in the middle) and another into the deck. This way, IMHO, it is invisible and tracks are free of glue.
The lower deck cannons would be difficult to rig, but you can try at least using the 'breech' line.