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I'm getting sand scraches showing through my next coat after sanding previous coats. They seem to go away after about the third coat. Will they show up later when I buff? I'm useing em6000 and sanding with 800 grit.

So - caveat first - I'm probably the least knowledgeable of those who will likely respond. But I've finished four guitars, so have made lots of mistakes!

I've been finishing with KTM 9 (I think, if not mistaken - EM6000 is also a waterborne laquer, right?) Perhaps they behave similarly.

Not clear from your post whether you're talking about sanding scratches that are on the bare wood (e.g. from before your finish) - or sanding scratches from sanding after each coat.

If it's the former, you're not going to like the answer - I've learned that preparation of the wood is perhaps the most important part of finishing - if you can see scrathes, you always will - the only option is to get back to the bare wood and sand smooth (e.g. no scratches)

If it's the latter, I'm not sure that that is necessary. I've sprayed four coats, sanded lightly with 400 wet and dry, then another 6 - 8 coats depending on how it looks. But ultimately you want probably a dozen coats minimum. I've found that the finish looks very "orange peely after all that spraying - starts to look good at about the 1600 wet dry stage. I've also found that I've had to go back to a coarser paper at times, since there were "sparkles" in the finish, where the orange peel wasn't completely sanded out.

Then, wet sanding with slightly soapy water with 400, 800, 1000, 1200 1600, then 2000. Then buff.

Corrections from the pros (and experienced) in the group appreciated and welcome.

Corkey, its scraches in the 1st few coats. I've been level sanding every 3 coats and have it close now so I'm ready to put the last coats on.

What you are describing is normal. It usually takes 2-3 coats to fill up the sanding scratches. They should not come back to haunt you.