Trolling motors are a workable and inexpensive means to move a DS when there is no wind and no current.
Do not expect speeds above about 3 knots, though.
Keeping the battery/batteries in the cuddy is preferred, as it improves the balance fore/aft. You may need to extend your cable to reach the transom, but if you do that, use a higher cross-section wire, otherwise you'll get voltage drops.
Batteries should be in boxes (to prevent acid leaks) and strapped down securely (in case of capsize, etc.). The motor can be kept in the cuddy and attached at the transom when you need it. (That's often how I use mine).
I usually bring two batteries. Extends the range and on days when I don't need the longer range protects me in case one of them decides to play dead just that day. Mine have lasted the full 7+ years, esp. as I don't actually need the motor every time and won't use it when not really needed.
I love the fact that even a little wind allows you to sail as fast or faster than the motor, so you don't use it unless it's the only option