Sanding woes

My trick is to apply masking tape around the gap, or area to be filled. Then apply the putty, working it into the gap. Let it dry then sand dry till it starts to feather out the masking tape. Then start wet sanding till the tape is feathered from the putty. Remove the tape and finish up with a seam scrapper and wet sanding. The masking tape protects the rest of the model. Have you thought of using super glue to fill in these areas? It works much better than putty.

I use the tape and putty method ... just watch what and where you are sanding and then use finer and finer grits of sand paper to polish out the scratches ... not always fun ... but it sure beats work !

I doubt 600 grit will show through the paint. That is unless you are painting NMF, which I haven't. Apparently it is very tough to hide minor scratches. If you are concerned consider a intial coat of primer which will fill in faint scratches.
HTH