There's a yellow arrow in the main window. Use it to point to things. It's especially helpful in email games.
Every deck, card, and piece has a right-click menu. Right-click the "Get" buttons in the Main and player windows to get pieces and events.
To move cratons and pieces in the Main window, first draw a box around them with your mouse to select them. Then drag them, or use Control-arrow keys (big moves) and Shift-arrow keys (small moves) to move them around. Using the arrow keys avoids some Vassal problems with dragging pieces by mouse.
When you populate a species, you may find it more efficient to put them directly on the table instead of on the newborn card.
In the Mutations window, click on the small gray squares to refill the display.
In player windows, it may work better for you to arrange a species in a row. Right-click "highlight" to make genotype cards stand out.
A toolbar button counts all creeples by color in the Main window. Look below the climate chart for the numbers. It's useful for scoring.
In the Events window, there is a empty deck space for a 5-card ET event deck. You don't need to use this deck unless you are playing the short or long "sudden death" game. For regular play, just draw cards directly from the larger ET deck. (All event decks automatically shuffle themselves.)
If you play the long or short game, then at the beginning of the last era, right-click the big ET deck and choose "draw specific cards." Choose "Chicxulub Class Comet." It's marked with an asterisk (*). Then drag a card (it will be the Comet card) from the big ET deck to the small ET deck. Finally, drag 4 more cards off the big ET deck to the small deck. Use the small deck for that era.
In each player window, you have a text piece. Right-click it to change the text. (You can clone it and delete it too.) It's useful to leave notes or to record your fossil and emotion points at game's end.