I've been asking for this for quite some time now. I don't think it's going to happen:
http://www.chess.com/forum/view/suggestions/combine-conditional-moves-and-analysis-board
This was just the latest in many requests....
Integrate analysis and conditional moves into main window
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It would be nice if I could use the main chess board as an analysis board / conditional moves. For example, I could make multiple moves just like the analysis board, and then I could press submit and it would submit either the one move, or all of the moves I've made as conditional moves.