Be Nice
To ensure that your message is well received it's important that it be written in an even-tempered tone. Being passionate about an issue and taking the debate about an issue personally by slinging expletive laced insults are two different things, with the latter not being constructive in the slightest. If you're unsure about the tone of the message you've written try leaving it for a few hours and then reading it again later, or have someone else read it and give you feedback.
Be Specific
The best feedback is specific feedback. If there is a specific MPA map you don't like, mention which one it is. If there is a specific MPA you don't agree with, mention where it is and why you don't agree with it. Mention what kind of fishing you do and where to give them an idea of how areas are being used. If there is a particular person or process of the Initiative you are concerned about, mention which one and why.
Offer Alternatives
Be part of the solution. Offering alternatives to specific issues you don't agree with is a great way to drive the process. Alternatives can be in the form of different MPAs, new regulations, etc. The MLPA Initiative has expressed an interest in creative solutions.