I have mentioned many times on this site that I don't like sealer....Sealer should only be used if you have a substrate that is suspect...or...you didn't prime the vehicle in the right shade of primer and need a sealer for more uniform color to achieve hiding with your base coat.
Sealer can be hot...sealer is another product to get dirt in...if at all possible, do not use sealer, it's not required when you do everything else properly.
Now, you have a problem...sand scratches where you have sealed the car. You can clear it, sand it and re-base over top of the prepped clear...no offense to anyone that suggested this, it will work...clear cost more than a 2K primer. Why not even out your substrate by applying 2 more coats of primer, it's cheaper, it's catalyzed and it's easier to sand. The base coat that you have applied will have gone past the recoatability or clearing window. Depending on the base coat you used, you can lightly sand the base coat with 600 grit wet paper, clean, tack and re base.
I hope this helps.