It really depends on what you are going to use those 12V ports for. If it's just for charging batteries then it would be best to run heavy guage wire directly to the battery terminal. If you are going to be running some high tech electronics that may not like a noisy source then you need a filtered line.

It sounds like you would like to only do the job once & want it done right the first time so I suggest that you go for all the above.

Run a fused heavy guage wire directly from the battery & add a BFC (big friggin capacitor) between it and a good ground. From there you can tap off to any number of 12V outlets that you feel you need.