The Lagoon itself is pretty shallow in most parts (see a satellite image). The channels that lead toward the pass that connects it to the gulf can hold fish during the daylight.
I've never caught a decent redfish in the lagoon, but I've never used a boat. I've seen pics of folks in kayaks and such catch some in daylight, so it's do-able.
I've caught quite a few speckled trout at different times. My best luck has been either around the piers at night, fishing by the lights, or near the pass. Around the piers, I like to use live bait - live shrimp, or baby croakers/mullet/bull minnows that I've cast-netted. I'll either fish them under a float, or (with the minnows) hop them Carolina-rig style.
At the pass, I've caught more fish on the gulf side in the surf on an out-going tide, but perhaps an incoming tide on the lagoon side would be just as good. Definitely watch the tide charts to see what direction the current is going.
Plan on takings some jerkbaits and Berkley Gulp shrimp for lures, as I've caught various types of fish with those. At the pass, you can also catch bluefish, Spanish mackerel, and ladyfish, but they don't seem to come into the lagoon that much.
I've seen a few flounder caught, but most were closer to the beach/pass area. I'm guessing they don't like the lower salinity in the lagoon.
Be careful for stingrays if you are out wading - sometimes there are lots of them in the lagoon. They will readily take live bait, but I've never caught one on artificial. You can sight fish for them. Really big ones are good to eat fresh, but I wouldn't waste my time on little ones, since they seemed like a lot of trouble to clean. My brother caught a 22-lb one off the Gulf Shores State Park Pier a couple years ago. The fresh meat was awesome - tasted like scallops - but the stuff we froze and thawed for later was barely worth eating.
Go to
http://www.gulfshorespierfishing.com/ and register for a free account. You can read the pier fishing reports (posted daily), and there are some reports of other areas that come in sporadically. That place is a wealth of information, and is searchable (similar to this forum), so you can read old posts and get all of your questions answered in a hurry. I would advise you to fish the pier as a first choice if the fish are biting, as you stand a chance of catching a lot more and bigger fish from there than you do in the Lagoon. I use the lagoon as my backup spot, but I understand if you are wanting to do some DIY adventure with your boat.
Good Luck!