First of all I think everyone needs way more information to help you out. Maybe something like screenshots of your team who you use for what stuff like that.
Some general tips though
Decide a main team for PVP and prioritize them. A lot of events revolve around PVP. Also they're most likely what you'll be using for instances with a few exceptions.
Second is probably your Survival Trial Ninjas you can start of with a tank a healer (preferably Kabuto) and most likey your PVP team.
Then your Ranked Battle Team.
It sound like a lot, but there's probably a lot of overlapping ninja you would use for several teams.
Lastly, the higher level you are the more time between level ups and the more time you can spend upgrading them a little at a time.