If you are needing to add a lot of brake fluid, on MY jeep it usually means that the cylinder's/pistons are pushed all the way out, and it would be a good time to check the amount of brake pads you have left. If the pads are all good, you might have a leak which is a very common problem with our older jeeps. If you are needing to add brake fluid frequently I would suspect a leak. Check the Hard lines, as these like to rust out.
Now, to actually answer your questions, Yes, you would add fluid to both sides of the reservoir, The small side to the front is for your rear brakes, and the larger side to the rear is actually for your front brakes. You would add fluid to the top, being careful not to spill it out of the top, (maybe about 1/4 of an inch from the top) and then push the gasket that is in the top back into itself until its flat. Then reinstall the cap.
Hope that helps