On the few I have built, I found it helpful to do the lock side first and get it nice and slim and very close to final form, then do a pencil rubbing, cut it out, and shape the sideplate side close to the pattern, most importantly making sure the tail and nose line up as Jim said. I then tweak each side to make them individually look best, and appearing generally consistent, without them necessarily being "mirror" images. Most orginal longrifles using two-bolt sideplates obviously made the sideplate to fit the lock, whereas today if you are using a pre-inlet stock you are trying to use a pre-set sideplate pattern with a lock and stock shape that weren't necessarily made to go with it. So you have to take some liberties, just don't make them drastic enough that they jump out. For example, I have found the same thing you are describing - i.e. if the sideplate sits high the sideplate panel might look big and clunky if you make it the exact same size and shape as the lock panel, so you can cheat a little off the bottom edge of the sidplate panel, give it a slight radius, etc. to help it visually. When you are at that stage of stcok shaping a 1/16 of an inch can (should) make a big difference visually with regard to the appearance.
BTW - I find the pencil rubbing/ paper pattern very helpful when laying out a patchbox as well - you can place it on the stock and stand back from the gun to take in the overall lines and see how it flows, and adjust the placement and angle of the patchbox until it looks right.
Guy