I suspect your CPA is telling you the amount of IRA contribution you can
deduct. You can still contribute up to $5000 (assuming you're under 50), you just wouldn't get a deduction for the entire contribution.
Since you're in the phaseout level of MAGI, I'm guessing your MAGI must be $101,840. That means you can deduct up to $2540 for contributions to each of your IRAs ($5080 total). But you can't mix and match the deductions - it's a per individual limitation. That said, if you contribute more than $2540 to each of your IRAs, you would get basis in the IRA for the nondeductible portion of the contributions (i.e., that portion could be withdrawn tax-free in retirement).
More in IRS Pub 590:
Publication 590 (2012), Individual Retirement Arrangements (IRAs)