You've probably already solved this, but, just in case, I'll take a stab at it.
I assume you can only download transactions back three months or so because that's all you bank keeps available online. So, I also assume you won't be able to manually download earlier transactions to a QIF file and import them into Quicken. Of course, you might want to confirm that last bit on your bank's web site.
To enter the earlier 3 months worth of transactions, you'd have to manually type in all of them from your bank statements. To avoid messing up your balance, take a look at what should probably be the first transaction in the register. It should be some kind of Opening Balance transaction. Just change that number to whatever you first bank statement shows as being its opening balance. Then enter each month's transactions and Reconcile them. That ought to do it.