1. we understand that in present case, you have admitted liability qua 3 (2+1) issues wherein payment for 2 issues was made before issuance of Order-in-Original and for 1 issue, payment was made after issuance of such order.
2. In this case, you can file form GST DRC-03A qua all 3 issues and knock off confirmed demand qua 3 issues (presuming that payment for 3rd issue has not been made from Electronic Liability Register). Once the payments confirmed qua 3 issues are knocked off, you may proceed to file appeal by declaring admitted tax as well as disputed tax.
3. If your issue does not resolve, then, the most advisable course of action would be to first file a Rectification Application under Section 161 of the CGST Act before the adjudicating authority. A rectification application under the CGST Act is maintainable only in cases involving an "error apparent on the face of the record" within the meaning of Section 161. Accordingly, while drafting the application, it must be strongly stressed that the relied-upon documents and payment challans were either already submitted along with the reply to the SCN/ or furnished during the course of Personal Hearing/ or otherwise available on the taxpayer's GSTN portal, which is accessible to the adjudicating authority.