Those are the key questions - is the deep water a lake, a reservoir or a river - and that will challenge your set up options. I've tried several and combinations of each.
On a river you have to consider the current. Individual lines on a decoy will need heavier weights else the current will drag them away. There's nothing worse then getting a spread set, the sun comes up and you see everything has shifted downstream on you. I agree with Superfowler, find an eddy or backwater and you'll be able to manage the depth with individual lines on your decoys not to mention avoiding having a tree float thru your spread and taking it away or your having to push the boat out thru your spread to chase your dog and a downed bird being carried away.
On a smaller river or where the current isn't so strong I've used "short" long lines - a dozen or so decoys on multiple lines each with a heavy weight - this displays a nice swimming group of ducks. Be careful with a dog though, on a river the lines are stretched out and a pup can get tangled up in them if he swims thru them. I attach a smaller weight on the long line where the decoy's drop line attaches to address this. Other than that you're back to heavier weights and a lot of string on each decoy.
On a reservoir if it is deep water you won't have a current or a dependable wind to keep a long line rig stretched out. I've tried it, even anchoring both ends and it is a hassle - time consuming, tangles, resetting, etc. I'm back to long strings on each decoy.
Either way a key challenge setting decoys with a boat is keeping the decoy lines out of your prop. Current, wind and the shoreline will present different situations that dictate setting up starting upstream and working your way downstream, starting in close to shore and working your way out, etc. Sometimes your best bet is to pitch the decoys out from shore then picking them up with the boat after the hunt.
It really, really, really sucks when you tangle up your decoys around your prop, in the dark, you're drift away downstream and you're scrambling to beach the boat with a push pole or standing on the back of the boat leaning over your motor cutting them away.
"A good friend will come bail you out of jail, but a true friend will be sitting next to you saying...'Damn, that was fun!'"