You don't have to change the colors from Hubitat, but if you do, you won't have to wait for them to get updated in Hubitat because the changes you make will be reflected immediately. As the other poster said, changes made from the Hue app (or non-Hubitat integrations) will need to wait for the next poll/refresh of the Hue Bridge from Hubitat in order to get the state. The default time for this is 60 seconds. Your actual time will, then, usually be less; you can also force it to happen when you know you're about to capture a scene by clicking "Refresh" on your Hue Bridge device (not the bulbs/groups but the Bridge).
If you like Hue scenes, Hubitat's native integration doesn't support them natively, as you discovered, so one workaround is re-creating them yourself in Hubitat. However, at least two community-created Hue Bridge integrations do support activating Hue scenes from Hubitat. I wrote CoCoHue, which has this feature, and an older option is Hue B Smart. Perhaps this way would be easier for you (but in both cases, activating a scene just calls out to Hue to do the same and you'll have to wait for the refresh interval to pass before Hubitat sees the current bulb states correctly; this does not matter unless you have apps/rules that need to trigger immediately based on such a change).
