I understand how reputations work. What I don't understand is the best way to go about ranking them up, which order to do them, and what items and bonuses I should get from each. I understand the last part is probably dependent on playstyle and ship/ship build. Oh, there's one more thing. Should I focus on one at a time or do multiple at once?
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You are going to want all of them eventually, and there are only so many things to buy in the reps, so too much of a surplus of marks for any particular one is not very useful in the long run, so balancing the need to keep the primary one(s) going with keeping as many of the rest going as it practical to do so is a good thing.
The best way to rank them up is to do the daily reputation thing, the hourly one is just a waste of marks for the most part since you get so much less bang for your marks from them. Once you get to level five in a rep you will see a job that reduces the cost of leveling that rep on any other characters on your account, make sure you do it since it only has to be done once for each reputation and really lowers the grind factor for alts reputation-wise. Going from five to six is a long trip, almost as long as getting to five in the first place, but it is worth it for the alternate energy type for the rep's special weapons and the buff it gives to the traits and weapons from that rep.
As for which rep(s) to pick to concentrate on, that is something whole books could be written about. The most basic rule of thumb is to stick with your preferred energy type (preferably a rep which has that energy type as its primary rather than the alternate you get access to at tier six), but other than that there are as many opinions as there are players.
Another *very* important thing to be mindful of: once you've advanced a rep to Tier 5, you unlock reduced reputation advancement costs for *every* other character on the account. Honestly, I did this so long ago that I don't even remember precisely how it works (or if the process has changed at all, since then) but, if you're working with a first character, you really do want to complete *all* of the reps ASAP, on that character, to make it easier for other later characters to advance whatever rep(s) you want, for them.