Awesome. I'm glad you are getting out there and actually experiencing the stuff first hand. Sometimes the learning curves are steep. This is one of those cases where you might be well served to watch someone else to rectify your board issues. I'll do my best to try and explain it. BUT... that said, I still get the same thing from time to time.
You normally don't have a ton of issues when you are running the bait on your close board (board A) with a short setback (say 45 feet). When board B (the outside board in a two board spread) is set at 70 feet back there is a big difference between the two setbacks and tangles are unlikely. Where you start running into issues is when your setbacks are close to one another OR, you are running similar depths. If for example, board A has a 50 setback and board B has a 60 setback, chances are high that, unless using some learned techniques, you ARE going to get tangles.
FYI, your assesment of waves and current is pretty spot on. That can have an influence. SO, here is what we do to try and mitigate the tangle issues.
Board A: Run it closer to the boat. Board B, run it down the center WAY FURTHER than you want it away from the boat. Let it ride in to position and then reel in the difference. When only running two boards, you can keep them further apart and this will avoid the tangles. When running three or more, it is VERY important to let that board go WAY out the back and ride into postion. This is a trick I learned after watching Kevin. Another trick (which I used this weekend and Steve got to witness). After you let that outside board ride up in to position. Start cranking it in a little ways. This often will produce a strike. Another trick is to let them out a little bit. Again, with following fish, this will produce strikes.
When the outside board goes off, and this is extremely important. DON'T start reeling. Let the weight of the fish pull the board way back so that it is almost inline with the other board before you start reeling. This is hard to do but works great. As long as there is tension on the line, you will not lose the fish. You still get tangles, it is unavoid able. Especially when you are running very similar setbacks. Running more than two boards isn't much different. Just have to pay attention to how much line you allow out the back of the boat to avoid one bait running overtop of another one.
As for towing fish. Do not feel bad. It takes a little while of watching boards for countless hours before you devolp a sense that you have something on. Sometimes, you are wrong but, more often than not, you are right. We towed a few around for 5 or so minutes knowing that we THOUGHT we had a fish on. We monitored the board very closely and eventually, saw somthing slight enough to warrent reeling it in.
Speed is another factor with this. A lot of times, some of these fish (salmon included) will be content swimming along with the baits. That reeling in or letting the board out trick is one of the best ones I have used in this scenario when I "think" there is a fish on.
The more you go, the more you know. I know that the navionics chips (although not great in some areas as we have witnessed) are pretty good for the bay. Just like with other electronics, (and I don't know why) some offer great maps of some locations and lousy ones of others. Lowrance maps have been great for the bay and other bigger bodies of water but they are lacking in the smaller lakes just as Navionics and lakemaster have their pro's and Con's.
All in all, you went out, were successful, and came back having learned some things and having questions on others. Once you get explainations to the questions, the picture get clearer.