You eventually get a feel for how much paint you normally apply, and how deep the panel lines need to be to avoid getting filled in. You must think ahead of the problem.
If it's a problem, you need to have a few tools in your arsenal, mainly a sharp-pointed scribing tool which can easily be used to deepen the original panel lines and sharpen them up. A set of curved riffler files is very handy, the triangular-section file is the best, it can help to widen the lines and it's fairly easy to freehand some new panel lines. My current project needed rescribing, and those two tools came in very handy, and my panel lines look great, even after paint.