it says i owe $3000 to manitoba this year, is that already paid? or is that on top of what ive paid in taxes this year?

Which line are you referring to?

If you entered all of the information from your slips and it shows $3000 in the taxes owed section of your screen then that is what you still owe. Check your T4 slips to see what it shows that you have paid (as deductions by your employer). It is possible that your employer didn't deduct any tax, or that you haven't entered the numbers for tax already deducted by your employer. 

Also make sure that you have entered the slips for the tuition tax credits.