Still not entirely sure of how to play the game...
It's actually quite easy. Clean the decks by either killing the enemy robots (fire at them or bump into them) and/or by capturing them (hold down right mouse button for "transfer mode" and bump into them), so that you'll get their abilities (for the good and for the bad). In the current version, the transfer will always be successfull...in the final version, there will be a subgame for the transfer like there was in the orginal game. Also still missing: elevators between the decks, consoles for accessing data etc...
Edit: In addition to the original game, there is a green arrow that points into the direction of the closest enemy.