In BUSY, you can file GSTR-1/GSTR-3B for different GSTINs by utilizing the branch feature. Alternatively, if you do not use this feature, you would need to create separate companies corresponding to each GSTIN.
Futher to reconcile GSTR 2A with BUSY data, you need to follow the steps:
Step 1: Go to transaction and then select GST misc utlities option from it.
Step 2: Then click on Download GSTR JSON data tab
Step 3: Then Select Download GSTR 2A option
Step 4: Now, Click on Download option for which month you want to reconcile.
Step 5: After download the GSTR 2A JSON ,again go to GST misc utilities and select reconcile GSTR data
Step 6: Then select Reconcile GSTR 2a either party wise or voucher wise
Step 7: Now, select the month for which you want to reconcile and then cross-verify the data.