Chris I've used a lot of different things but my go to set up is to use CA gel that I put on a piece of playing card stock, then use a toothpick or I have a this piece of pointed metal to dab the cement to the part. A long sewing needle with the eyelet either cut in half works great. Its just one of those hazards we deal with and move on, my biggest concern is dropping the part or worse yet breaking it.
Chris my main adhesive is Tamiya Extra Thin, I agree with CN Spots that almost always I can get away with it but if a little more comes off the brush, I use the tip of a paper towel to wick away the excess that leaves just the right amount and hardly ever a mess.
Its a pain no matter what the method, there very small fragile parts usually in an awkward area.
Hope it helps some. Terry