The reality is that most every car gets skimmed with filler. The goal is to get them as straight as possible, and that's the only way (in the real world) to get them actually straight.
So, how do you go about skim coating a panel that is too large for one fill? First, a panel shouldn't be skimmed until smaller areas that need additional filler are 'roughed in'. Once that is done, the entire panel should get a skim coat.
Filler should be shaped before it is completely dry (covered in a previous post). With that in mind, break the panel up into manageable sections. Fill an area that you know you'll have enough time to really spread the filler properly, and get that area blocked out before moving on.
Filler should only go over 80 grit or finer, so get your area roughed out in 36 or 40 grit, then switch to 80 grit to get the shape closer. Once it's in 80 grit, and it's pretty close to being correct, move on to the next area.
Fill the section right next to the previous section, over lapping just a little bit. Fill it properly, rough it out with 36/40 grit, finish blocking with 80, and move on to the next section.
But what about the scratches? Yes, blocking the next area with 36 grit will get into the 80 grit area, but, it's ok. You should have left a little extra material anyway, so when it's all skimmed, the entire panel will get blocked out with 80 grit. Don't over think it. Also, don't try to get the entire panel skimmed at once before sanding. Block sanding cured filler is a waste of time, and the results typically aren't as good.
So basically, just fill one area at a time.