AngeloEvs: You can form a 'step' along the edge of the new section (or the existing section) using a 'joggler'.
Not cheap (for a hand tool!) but solves the problem you are experiencing. The head also rotates and acts as a hole punch. These punched holes are on the panel that sits over the stepped section and are your weld points (almost like 'spot welding'). Useful tool as it enables a quick means of adding mild steel right angle section to panels that need flanges!
Was £60.89, Now £43.90, Amazon.com, July 2010
AngeloEvs: A joggler is a hand operated forming tool/hole punch. It allows you to create lap joints and have the two panels at the same height.
In the pics below (using odd sheets of mild steel to demo), I have created a step along one panel by running the joggler along the edge and squeezing the handles. You can see where I have stopped as the step dissappears. Simple to do but run along the edge a couple of times.
The other panel has series of holes punched, once again, easy to do - just rotate the head on the joggler (as easy as punching holes in paper!)
Overlay the panels and voila, you can puddle weld each hole (easiest form of welding for a newbie) and later weld along the joint (or lead load) if you think appropriate. Most often a few tacks along the way is sufficient unless the panel is subjected to a lot of stress. Flush any high spots with your angle grinder and tap back any high spots in the panel with a block of wood if necessary.
Some panel work involves slight curves across the X axis and the 'step' can sometimes interfere with it following the natural curve of the panel youer welding on to. If so, I cut slots into the step (at curve points) and this allows the stepped section to follow the line of the panel your welding on to. Most of the time its not a problem but worth mentioning.