You may be new to an Allen such as this. If the person who set up the existing presets was registering some typical classical registrations, then surely the lower manual (Great) was intentionally made louder than the upper (Swell), and perhaps the Swell-to-Great coupler is part of each registration, which would also contribute to that.
If you are wanting to set up someregistrations with the upper or Swell manual louder, just Cancel all the stops (press the Cancel --"GC" or "0"piston) and then draw several stops in the Swell division (majoring on 8' and 4' perhaps)and only a few in the Great. Experiment until it sounds the way you want it to. Draw some 16' and 8' stops in the pedals and you should have a respectable generic registration.
If you want to save your own presets, just hold in the "set" piston and tap one of the General pistons (numbered 1 - 10 at the left end of the piston rails, under the two manuals). Then you can instantly recall the registration you have set (provided the combination action is working properly. That's a pretty old organ and it may have dead batteries unless someone has been maintaining them.)
Best of luck.