There is indeed a help page for the new online playing feature. There is a link on the upper right corner of the page (both in the game room and in the actual playing table) that takes you there. Please read it carefully. We'll try to update it and improve it with your feedback.
As mentioned on the help, to have your base in your Removed from game deck, you just need to put that card in the deck's Base section. All other cards should go into the Deck section and will be in the Deck when playing (already shuffled).
Regarding the way to finish a game, that has just been added. There is a link next to the Help link that lets you choose how to end the game: by declaring your opponent the winner, by requesting a tie or draw (your opponent has to confirm he agrees with that), or by aborting the game (for example when your opponent leaves or gets disconnected for some reason).
Hope this helps. Please let us know if you have more questions. And do report to us any problems you encounter with the interface so we can fix them as soon as possible.