Just to follow up on this thread - here is where I am now:
1) Apple have agreed to refund the purchase cost of NavGate and associated in app-purchases (claim made yesterday, no reply recieved to the initial Pioneer Support call). I am now using "Nav4Free" with some upgrades - this works a treat.
2) With regards to the sub woofer pre-out problem, this is now resolved - looking at the manual link in Dannys post above the solution is in there, but the manual is somewhat ambiguous about it, for reference if anyone else has this problem you have to do the following: a) Disconnect Ipod/Iphon