Paying invoice from another company code

We need to pay for invoices from company code A through company code B. How do we do that. Can we achieve this by setting up the variant in RFFOUS_C by putting in sending company code as A and paying code as B. Or  additionally do we have to maintain it in OBYA also.
But in my case if we have to maintain it in OBYA, I cannot do it, because there are GL accounts setup in OBYA for intercompany clearing. I dont know if there is a way to create new entries to maintain this in OBYA? Please advice.

I think the steps maintained by Paul is all you need to configure.
Lets take your scenario when GL clearing accounts are set in OBYA for cross-company between Company code A and company code B.
And company B is the paying company, then a vendor invoice (say Cr$100) in Company A will be cleared by payment run by following entries in the 2 companies
Company A
Vendor Dr $100
GL clearing account (in OBYA) Cr $100
Company B
Cash Outgoing Bank Account Cr $100
GL clearing account (in OBYA)
Lets assume that company A will pay back the money to company B on weekly basis. And lets say by that time company B has paid $100,000 onbehalf of A.
GL clearing account (Balance in company A) Cr$100,000
GL clearing account (Balance in company B) Dr$100,000
So, after a week company A has done a wire payment of $100,000 to company B to settle the due to. This can be captured by following clearing entries
Company A
GL clearing account (in A) Dr$100,000
Cash Outgoing Bank Account Cr $100,000
Company B
GL clearing account (in A) Cr$100,000
Cash Incoming Bank Account Dr $100,000
This way your Inter-co GL clearing accounts are cleared, and the Bank outgoing and Bank incoming will be cleared when you will do you Bank statement posting
Thanks
Ron

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