The advantage of using Tv is, of course, that the camera adjusts to changing lighting. This can be helpful in this situation not just from clouds, but from either the shooter's boat or a subject boat changing in respect to the sun -- you could either blow out highlights or get overly dark shadows.
The disadvantage is that you have to pay close attention to what you're metering and adjust your exposure compensation whenever you do get a change of lighting. You have to decide how to handle shadows, changing sky tones and backlighting and adjust accordingly.
The advantage of Manual is, of course, that given consistent lighting, your exposure won't be thrown off by incident lighting changes on your subject, background, etc, and so your images will be consistent for that scene. But, you have to be on your toes whenever the lighting changes, as in when your boat turns into a new direction relative to the sun (and are shooting a scene/subject with new lighting). Again, you have to pay attention to what you are exposing for, and, like in Tv mode, use your thumb wheel to adust your aperture (assuming you want a consistent shutter speed). If you don't do that, the camera will make no automatic adjustments for you and you could lose shots until you catch up.
I think which is "better" is up to the shooter. I've been using Manual mode for a lot of my shooting, especially when I have a scene with consistent lighting. But when I forget to adjust for light changes things can get messy. My other "normal" shooting mode is aperture priority, which tends to work well with me in outdoor settings with low, changing lighting. I'm still practicing a lot with manual, but I have something to fall back on that works for me!
If I were the OP, I'd first of all get the lesson drilled in of how the meter works (and why these pics came out underexposed), so that exposing for say, the sky or white sails or somewhat medium water came automatically no matter what mode you were in. Try this out in both Manual and Tv and see what gives the best results. It's not that the 5D was underexposing per se, but that the 5D was very definitely and obviously rendering those white sails grey. So, if you practice your exposure before your next "real" shoot I think you'll be happy with the results.
As far as RAW vs jpeg is concerned, that's another matter of personal choice. Many shooters with clients who want to see results "right now" opt for jpeg, as you do. However, RAW developing/converting software today is very efficient -- you can make batch development adjustments to exposure, contrast, saturation, white balance and sharpening in just a few clicks and then output jpegs in just a few more clicks. Plus, RAW has better lattitude in recovering both highlights and shadows, so that slipups have a greater chance of being keepers!
Well, OP, you do have a great camera! Get over these "little hurdles" and I think you'll be thrilled!