ok, i figured it out - maybe someone's having similar trouble though?
1 Enter the conditional moves page and select 'Deep Mode'
2 You have to specify a position you want to reply to, so make a move for your opponent
3 Click 'Record Conditional Move' BEFORE you input your response
4 Specify your response to the position by making a move and click 'Submit'
5 Return to step 2 as necessary
I understood it once I realized that instead of inputting a series of conditional moves you are specifying replies to particular positions. These are irrespective of move order. This is a much better system than i'm used to for a simple reason. On the site I'm used to you often have to input the same moves several times because the opponent might vary his response on move 3, for example, leaving a given variation. This process is sidestepped by dispensing with variations and setting responses to particular positions - nice work RHP!