I've never used the Woodland Scenics for water.
Might be worth searching throu youtube to see what other people have shared.
Yes. paint the wood base. I'd probably use Krylon, and in flat black.
However, I'd suggest a trip to the big box home center first, to go look at Trim. See, your swamp will need some depth. That trim will help define the depth, and will provide a much better finished edge than the plain plywood will.
Swamps are generally a mix of high and low spots, so you probably need to build up some high spots. Many materials will work for this--celluclay, Durham's Water Putty, hydrocal, even plaster.
However plaster--and it's cousin premixed spackle--are some of the hardest materials for a first-timer to work with. So, any of the previoulsy mentioned items are likely to be easier to work with.
Paint will be your friend. But, over your groundwork, you can use inexpensive craftstore paint and use darker colors to show depth, and lighter to show shallow.
Cull through the diorama videos on youtube; do a lot of google image search for swamps.
Also, et this be a test. Let it be astand alone, so you have not committed a model with your blood, sweat, ad tears into it. If you can model a swamp all by itself, you can make a diorama of anything.