you can always create manually new edges to connect faces/create new faces
for example you can cut the connecting structs you were talking about, and connect manually the secondary section to main hull.
If you want to make an hole in an extrusion, you can for example select the face where there will be the hole, extrude with 0,0,0, scale proportionally the extruded face, extrude again with with a negative Z, connect vertices manually to the other side, use erase faces tool to open the hole... but there really are many other strategies.
and booleans don't necessary screw your model, with some experience you should be able to anticipate many probs, but surely you will have always to spend some time to clean double verts and weld unuseful ones, that are the two kind of probs you have with booleans...using boolenas just mean to know how to avoid/correct them..i hated boolys too in past, but now i can use them pretty well