You can find a lot of discussion of this topic here. Lots of folks trim as much fat as possible around the point and flat and then leave them together. Some cook separately. I've done both and the thing that I found important is that they cook differently, and the flat is the important part to get done right. The point is going to be OK pretty much no matter what, since it is so fatty. I'd say trim fat to around 1/8 to 1/4 inch everywhere, leave them together, and make sure the flat is done at at least 200F. The point makes great burnt ends (another search for you) and there is nothing better than a tender and juicy flat basted by the fat from the point during the cook.
Another point when buying a packer is to look for a flat that is as uniform in thickness as possible, to avoid the problem you mention. The thicker the "small" end of the flat, the better.
I know I'm infringing on the expertise of a lot of other people here, and I'll happily defer to their opinions if (as I hope) they jump in.