On the Ebills page, after logging in, select "Student Account"; that should show you a detailed listing of your fees and any aid that's already been applied to your account. That should let you know if your financial aid is properly being credited towards your fees. If it's not listed, you should be able to call the Financial Aid office and ask them what the issue is.
As an example, here's what my billing statement looks like (with personally identifying information scrubbed out; nobody should ever post ANYTHING that could identify you to the interwebs). At the top are the fees; below that is the $100 I paid to say "I'm coming" and is credited to my account; below that are my financial aid entries. Note that a negative number in "TOTAL DUE" means that they're going to be dropping money in my direct deposit account once Sept 21 rolls around (my aid currently exceeds my fees). If you have a negative amount showing there, you won't need to pay anything.
Code:
20-AUG-09 Summer Orientation Student Fee 85.00
21-AUG-09 Fall Quarter Registration Fees 3,105.65
21-AUG-09 Fall Student Health Ins (SHIP) 349.00
- CURRENT PAYMENTS -
21-AUG-09 Statement Intent Reg-Fall 100.00
* CURRENT BILLED BALANCE * 3,439.65
(Loans) 3,483.00
(Scholarship) 1,000.00
* FINANCIAL AID BALANCE * 4,483.00
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
PAST DUE: .00 FUTURE BALANCE: .00 TOTAL DUE: -1,043.35
--------------------------------------------------------------------------------