MY suggestion is to stay in Yarmouth as little as possible.... The only saving grace is that your in Yarmouth PORT, that little word means ALOT.
Seriously, the centeral and upper cape,are not cape cod. The rooms are cheaper typically down that way, but you gota hit Chatham, Orleans and Provincetown for the 'real' cape experience. That is alot of stuff to pack into just 2 days, see things, enjoy vaca, and be ALIVE for it.
Are you hauling the boat all over the NE for this trip? There is a nice harbor right down the road from Y.Port. Fishing spots 15min boat ride away in CC bay.
http://www.northsidemarina.com/