If you are going for all the achievements in the game, I recommend having one game where you have the Death Sonar skill, and one where you don't. The Death Sonar is a useful skill obtained early on in the game, and there are achievements related to acquiring and using it, listed below:
But there is also one achievement for getting to a certain level without having the Death Sonar and, as this level is very far into the game, I recommend continuing with that game save to the games end. This will probably be slightly more difficult a playthrough but it is certainly manageable. For reference, this achievement is:
Of course, if you aren't interested in those achievements, I recommend getting the Death Sonar for both playthroughs. It's really up to you.
Now it is just a matter of completing the game twice, this must be two entirely separate playthroughs starting from Home Bay and working your way to the end and final boss. The game allows you to save wherever you like so save often and in good locations such as when you pass difficult sections or when you have a good amount of health or air. If you die, you'll be sent back to the start of the level, so if you have a mid-level save you may aswell quit and reload the save.
Also, remember to save once you reach the final boss, as dieing here will send you back to Welcome to the Machine, the previous level.
If you're having trouble passing the levels I recommend these resources:
Maps:
http://ecco-darksea.us/?p=25Walkthrough:
http://www.neoseeker.com/resourcelink.html?rlid=83231&ri...