Will I be getting two check when I file my taxes?

That currently is not known.  When the stimulus payments were issued in the spring (and in the current second issue), the amounts were paid out even if someone owed (one exception was if someone owed back child support).  But no clear indication has yet been given as to whether the stimulus will be paid out regardless even if one otherwise owes on their 2020 taxes or if they owe back taxes from prior years.  The IRS will no doubt provide additional guidance on this.

@Alvinjnunez @DanielV01 - the payments are 'advance payments' against the 2020 tax return, so if you work through the 2020 form 1040 schedule, the stimulus appears in the payment section ( line 30 of lines 25-33) that reduces the taxes owed.  So while I agree it's not totally clear, based on how the schedule works, it's clear that if the completing the 2020 return results in a refund due, it would work the same and be netted against outstanding taxes from prior years.  

The IRS sent out the 2 stimulus checks even if you owed taxes as that was the rules for the Payments, but there is no rule I could file about the Recovery Rebate Credit which a payment on Line 30 (so within the lines 25-33 section) .

Again, not clear, but does point in one direction.