Can anyone clarify exactly what perimeter means compared to low-post?  I've always thought of it as the ability to shoot a 3 pointer but does it also apply to long jump shots too?  

Also, if you have a 85 rated perimeter guy with less than 20 low-post, would you recommend always setting the 3 PT frequency to +2?

Yes, PER applies even to short jump shots.  I believe that there was a note to an update that suggested that you should think of LP as inside scoring and PER as outside scoring, but everything in between is determined by a blend of both.  ATH, SPD, IQ & BH make a difference as well.

For your example, +2 is not necessary.  I would look at other ratings too.  If that guy had no ATH or REB and was poor at FTs, then sure, but otherwise +1 or 0 would be fine.  On the other hand, if that guy had high ATH, good at the line, and your opponent was likely to attempt to defend the perimeter, then +2 is giving away too much.  The key is to watch offensive efficiency.  If he seems to be hitting 3's at the same % as 2's (or at least 38%), then let him jack them up, but not otherwise.

Per is jump shots LP is everything else including postups, layups, floaters, and just generally finishing at the basket.

It regards to + settings if you put a guy at 0 they tend to naturally gravitate towards what they are good at. A high per/low LP player on 0 will take a lot more 3s than a low per/high LP player at the same position.