You're saying the account you've been playing on (your Vita) isn't the same account as in different user name then your PS3, right? If that's right then yes, you won't be able to access your existing content from your Vita account since it is a different user name.
All you do is go on the PS3, and turn it on. Depending on the PS3 settings, you'll find where it says "Create New User" on the left side of the XMB UI.
Click that and just choose Existing PSN user name. Log in with the Vita account and there is your Vita account on your PS3.