If it were me I'd go ahead and use some of the same water from the 55 to the 90, if only to help lessen the possible shock to fish. It is not so much as keeping the same bacteria, but maintaining a pH and so on that is similar enough to what the fish were used to. There's always going to be a little bit of fluctuation for the fish to adjust to, but there'll be less of that. Consider it more like a 30-40% water change into a different container.
Otherwise, go ahead and fill up your 90 with new water, then treat your fish like you just got them from a pet store and acclimate them that way. Much riskier though, with then having to later worry about a water crash.
If you can, use the same filter media from the 55 to the 90. That'll help with the tank cycling. Especially if you decide to use all newly treated water.