You should be fine, just take care to grip the screwdriver so you don't drop it and ding up the top. Happens easily if your not mindful of it.
Also, like all adjustments on a guitar, go slow. Don't make any drastic adjustments at once. Small amounts, retune, check playability, continue to adjust if needed.
I don't have two piece bridges, I have all stoptails. But I like to set the bridges really, really low. Actually most of my bridges are down all the way. Then I actually use the truss rod to get action where I like it, which is extremely low. Most people who play my guitars feel like they're too buzzy, but to me they sound great through an amp and are much easier to play. I know it's out of PRS spec but I'm sure it's not hurting anything and its just personal preference.
Try lowering the bridge until the higher frets begin to buzz, then bring it back up so they don't buzz anymore. The playability of those upper frets should only be affected by the bridge, and not the neck (more or less). The middle to lower frets will be affected by the truss rod, as well as the bridge. If you think you need the neck adjusted, have a tech do it or do a bunch of research, youtube videos and whatnot before you get in there. You can get in trouble with that if you don't know what the deal is.