I want to enroll 2 aws accounts which are created in an aws organization under lets say Root Account 1 into the Organization Units created by Control Tower in Root Account 2.
The main problem here is that the two root accounts are totally different accounts and they are not linked to each other in any way.
An AWS Organization always has exactly one management account. The management account is the one hosting the AWS Organization, and also the account that you have to call all AWS Organizations API operations on.
Control Tower is an AWS Service that orchestrates AWS Organizations and a bunch of other AWS services for you as a convenient starting point for basic landing zone needs. AWS Control Tower itself can be hosted on another account than the management account.
The scenario you describe sounds like Root Account 1 is the management account, so even though control tower (from account 2) created the OU, it created them in the AWS Organization management account (account 1). So enrolling additional accounts in the organization (account 1) via control tower (account 2) should not be a problem at all.