....over the years I grew a collection of ships. I got bored of always using the same ship I happen to like variaty.
I also have 9 ships and a shuttle. I found that it was easiest to make a spreadsheet grid - Ships names along the top, boff names on the side - and then plot out which ships need what type of boff and what powers would overlap. For example, you want two copies of Tactical Team on most ships, but sometimes you need beams or cannons or torps and the ease of a spreadsheet helps you see who can be assigned to which ship.
That having been said, lots of people on here will poo-poo the idea of playing from a spreadsheet, and I agree sometimes you have to swap boffs on the fly depending on the situation. However, unless they post a better suggestion of how to effieciently assign boffs to multiple ships, they're just full of hot air.
The standards that I do have on every ship is one Engineer boff with EPtS & RSP, one Sci boff with two copies of HE, one Tac with two TTs, and fill in the rest of my boffs depending on ship function. Everyone's different, though, and your playstyle may vary quite a bit from what works for me. Re-read erad84's post on the first page, then see which boffs you have on every ship, and which ones are just situational; After that, just assign accordingly.
Have you hit the limit of purchasable BOff slots yet?
Those are the only two ways around it, stock up on BOffs and use the same BOff in multiple places when possible (for example, my Sci has a BOff with Torp Spread I (ens) and BFaW II (Lt). She's slotted on my Luna and my Gal-X, and will most likely find a home on whatever other sci / cruiser I own, because there's barely any Sci / cruisers that use the Lt Cmdr Tac slot, and if I do get one of those I'll either respec a different tac BOff for that ship, or tweak her third power to fit that build...
Yes, I'm going here. Iconic / "hero" ships, I'm talking Galaxy/Defiant/Intrepid here you TNG-era fans, get a T6 version, then ALL the hero ships (Connie, Miranda, NX, etc.) need one too. I'm a ToS fan, and proud of it. This is a themepark, let me enjoy my ride or none of us deserve one...