Any length trip works for the BWCA, but for kayaking I recommend day trips in order to ease any portages.
Do you plan to camp or stay in a cabin? If you plan to camp, you will need overnight permits for the BWCA, unless you camp outside the Boundary Waters. If that is the case, you should get your permit ASAP. More information is available here:http://bwca.cc/tripplanning/reservations.htm
If you stay at a cabin or camp outside the BWCA, you will only need day permits (free).