As stated before: get deep down into google earth or other sattelite maps. they give you a nice idea of shallows and mangroves.
Lodging... the cheapest places are true backpack huts. for example we had a room in nicaragua starting at 12 dollars a night (3 guys, one slept on the floor) for the room.
The cheaper the ride, the more DIY and chances are great it turns out to be totally different from what you wished for. But that doesn't mean it sucks. it can be awesome just exploring, sipping rum, talking to backpackers, drinking beer, eating local food (and getting it out of your body in all liquid forms, from every exit/entrance your body has), boozing rum from the bottle and even meeting true hippies. Oh yeah, and I caught some fish too
Last year we had a very nice time in nicaragua, but the fishing was not what we hoped for. That's the game of DIY.
One piece of advise...: If you're totally new to fishing/spotting/recognizing potential area's, than it could be usefull to spend more money the first trips to get out there with someone who knows (and probably wants you to pay for the knowledge).