I have run into a snag today. I've been changing my strings just fine not having to worry about gauges on my old Squier but I think this is the first time I tried changing gauges (from 10s to 9s) on my SG. The problem is that the string height was just fine with the 10s on but when I put the 9s on it caused the strings to become flushed against the neck and they're pretty much right on top of the frets now.

What seems to be the problem? (I normally also string them full tension but today I gave them slack) I haven't checked the saddles yet on the bridge if that may be the problem.
You have to adjust the truss rod since the tension on it is smaller now with the lighter strings. Not a big deal and you can probably do it yourself.
Counterclockwise - but slowly, don't force it if it's stuck and only do a quarter of turn per day, then tune the guitar and wait 24 hours to see how it feels. repeat until you are happy.