Using all the books, even for character generation, can overwhelm your players and you. What I'd suggest is to pick your theme, then use the book plus the core rule book based on that. If you're going to do scouts, use the scout book for extra careers. Privateers? Scoundrels. Traders? Merchant Prince. This will also help your players focus on the task at hand, as the expanded character options will mostly be in the direction you want the campaign to go. Sure, you're always going to have that one guy that makes an ex-pirate in a scout campaign even if you give him 20 extra scout related careers to choose from, but there's nothing you can do about that! (Well, actually there is...house rule, last two terms have to be scouts...I've done that before, it also easily explains why the players all know each other, they spent the last four to eight years together prior to the campaign starting)
Each of these books will also greatly expand information and rules for those specific types of campaigns, but will have limited usefulness if the campaign direction is unrelated. There's really no reason to use ALL of the books, as most of the material inside them isn't very useful unless you're running a campaign specifically geared in the direction of each book.
High Guard isn't really useful for adventurer type ships/characters/campaigns, apart from expanding ship building with some new stuff and a few changes to space combat rules. Merc doesn't add much either for a standard campaign besides equipment and some extra combat rules. v2 does have the entire list of weapons from all the books at the back, with corrections, which is nice though. Adding either of these shouldn't change your campaign much.
Other than that, unless someone REALLY wants to play say a psychic or a robot, or anything else for that matter, leave the rest of the books out that aren't related to the campaign. Bring things in when they are relevant perhaps, like if your scouts start trading regularly you can start using the expanded rules in Merchant Princes.