We have a Electrostatic Pummeler with 4 +1/+1 counters on it and three energy counters. We activate Pummeller's ability. What are its P/T once the ability resolves? I am confused if it is 6/6 or 10/10.
+X/+X is applied on sublayer 7c while counters are applied on sublayer 7d. Yet it seems logical that as the ability resolves and continuous effects are applied all the time X will be 5.

I think I am doing layers wrong. Is there a rule I missed?

In the situation you describe, Electrostatic Pummeler will give itself +5/+5 and end up as a 10/10.

The problem you're encountering is that you're trying to determine how big a boost the Pummeler's ability should grant in the middle of working through the layer system, when that's not how the effect works. Pummeler's ability doesn't continually update the bonus it's granting as the game moves on–instead, as described in CR608.2g, it determines the size of the boost it needs to grant only once, as the ability first resolves. After that, it will continue granting that same boost no matter how the Pummeler's power changes, and no matter where in the layer system that boost is applied.