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I switched to a new clearinghouses & for some reason now when I post my payments revenue management is applying the secondary payments as a the primary payer.

Revenue Management matches the payer by Primary Receiver and Secondary Receiver Claims Payer id in the Insurance Carrier record. Make sure both of these values match what is used by your new clearinghouse on both your primary and secondary insurance carrier.

Navicure sent me a list of all their payers & it included a payer code (payer id) & a payer entity. Where in Medisoft would I put the payer entity code?

In Medisoft go to Lists -> Insurance -> Carriers -> double-click the insurance carrier -> EDI/Eligibility tab and enter into the Claims Payer ID field on both the Primary Receiver and Secondary Receiver frames.

Thank you Gavin...

Do I put anything in the EDI Extra 1/Medigap field?

Enter the MediGap # there. You can get the list of MediGap ids from your Medicare intermediary.