Two notions that you can roll around your head:
One, instead of "sparing", try "controlled" -- apply glue with a syringe or other applicator that lets you put down an even bead. Remember that it washes off with water before it's dry, so you can try and try again.
Two, go through some of the build threads on the full-fuselage stunters. I haven't done this yet, but it appears that the super-zoot way to do this is to glue the canopy into a fitted notch in the fuselage with epoxy. At this point you'll gave visible glue, so then you mask off most of the canopy, you put a fillet around the bottom, and you paint the bottom 1/8" or so of canopy, neatly (one hopes) covering up the mess.
I haven't actually done either of these, so take my comments for what they're worth.