It's still usable. Just flip up the armrest or reach around it. It's sort of a pain but the storage you get from the armrest is nice. I bought one of those collapsible cup holders from ebay and screwed it to the subwoofer enclosure.
The front one is still pretty easy to get to. You can get to the middle and rear one too but it is a little tougher without folding it up. The armrest is such an improvement that it is not a big deal for me at all.