Howdy and welcome to the forum! I myself returned to modelling recently and I've learned a bunch through the forum and through the other resources out there. I was puddying last night thinking about this very topic. If you haven't yet, check out Swanny's page at
www.swannysmodels.com. He does some awesome work, and puts a lot of builds online which I have found to be an excellent resource. He has included a section on puddying. Click the "tools & tips" link, and then on the "seam repair" section (or just go to
http://www.swannysmodels.com/Seams.html). I should have done this last night but I was lazy and now I'll be sanding. He outlines a method for seam repair that should at least answer that dilemma. In addition, I know that people will scribe lines (he has a link about this too -
http://www.swannysmodels.com/Scribing.html) where raised lines have been erased by sanding. Good luck and have fun
Jon