How to use chess engine to find what moves to focus analysis on

For this phase, I start my computer and let it run until it has gone through the whole games. I use it to get a list of all chess engine evaluations for all positions in the whole game. And also to throw in recommendations for different draws where the move was evaluated as a blunder by the chess engine.

I actually use two different tools, but only one is needed. They both have advantages and drawbacks. Chessbase has an easier interface, but Aquarium has a little better analysis functionality.

• With Chessbase, I need to use blunder-check. This is the only way I know in Chessbase to get both an evaluation written for all lines, and alternative moves inserted as part of the analysis.
• With ChessOk Aquarium it is done with full game analysis.

For both, I need to tell the engines how long to think, and what to consider a move to insert alternatives for.