Ok, so you have an acrylic paint over formica, and a thick epoxy coating over the acrylic paint to protect it.
I presume that this is the epoxy coating you used:
http://www.newparks.com/parksclear-pg.html
http://www.newparks.com/PDF/71540-Instructions_FP.pdf
When you work with oil based finishes, you'd want to apply the second coat before the first coat fully cures (or within 24 hours) to ensure good crosslinking between coats for maximum adhesion.
However, you're dealing with a two part epoxy here, and epoxy is well known for sticking well. I don't believe you should apply any more epoxy before the first application has fully cured. If inter-coat adhesion was of any concern, that PDF file would suggest you pour the second coat within the 72 hour curing time of the first coat. They don't suggest that, so I think you're better off to apply two completely separate coats and rely on the high adhesive strength of epoxy to ensure good adhesion between coats. (just make sure the surface of the first coat is clean before pouring the second coat or any dirt is gonna become permanently encased in epoxy)
Also, you say you need more epoxy in certain spots. If you just poured more epoxy onto certain areas without covering the whole counter top, then you'd see the edges of the areas covered with a second coat. I think you'd be better off to buy enough of the stuff to cover the entire counter top completely with the second coat rather than just trying to cover certain areas. Even if you have to wait to get more epoxy, I'd ensure you have enough to cover the whole top and not just the areas you think need more epoxy.
The attached PDF file says to wipe down the first coat with alcohol or acetone before pouring on the second coat to ensure maximum adhesion between coats.
So, I'd follow the instructions and allow the first coat to cure completely, and then wipe it down with acetone, allow two or three minutes for the acetone to evaporate, and then pour and level your second coat.