This is two part question. First some background information. I am currently world building - hobby of mine - and I kind of hit a brick wall in terms of philosophy, ethics and planetary colonization. So the first question is based on a young Earth scenario. The planet in question would be analogous to Phanerozoic Earth, though the planet is inhabited with aquatic life, the land has not been "colonised" yet by life. So if a human were to inhabit a planet what would be the best way to do it? Do we just throw in typical Earth life or do we create creatures using the already pre-existing life as a toolkit. There is another question as well, this planet would have approximately have 88% of its surface covered in water. Would such a planet be even worth inhabiting?
That depends upon the planet that humans find. Since we don't know much of other planets outside of our solar system it would be very hard to come up with a plan until humans actually find one to inhabit. There won't be a large human population that gets to that planet so it would take a very long time to overpopulate it. Earth is 75% water and we have billions living here so that should suggest that your water world planet would be worth developing. Of course I do hope the other 12% of your planet is land and not frozen waste lands like in Artic.
Your biggest problem that is generally overlooked, is microorganisms. There are lots of them by the time you get fish, and they can be very aggressive. You'll want to have a really good sampling of those in laboratory conditions to see how compatible they might be - and how pathogenic they might become - with Earth-based organisms. Conversely, you'll want to study the scads of flora and fauna to which humans are a natural host, and without which a transplanted human will die. If our intestinal bacteria get into the local water, you might have a dead planet before VE Day.
Like this? http://masseffect.wikia.com/wiki/Eletania Another question. How hard would it be for the new habitants to redevelop into a space faring race if they ever went through some form of dark age? Island Nations tend to be resource poor. So if most of the land are effectively islands... resource gathering be fairly difference. Right? Or am I missing something.
Look at Japan, Australia and Indonesia for they are almost self sufficient. Adaptation is going to be the way to go to make any place suitable for humankind to progress. New technologies would certainly be forthcoming from newly inhabited planets and perhaps they would be able to make hydrogen for their fuel to energize their new found society on new found planets like you are suggesting.