Steps for Inter company transaction:
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Create Customer named as Company (e.g. Company A), check Is Internal Customer option and select appropriate company (e.g. Company A). Add company under Allowed To Transact With
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Create Supplier named as Company (e.g. Company B), check Is Internal Customer option and select appropriate company (e.g. Company B). Add company under Allowed To Transact With
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Create Sales Invoice using customer created as above (e.g. Company A) : System will automatically show Inter Company Invoice option under Create after submission.
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When you click on Inter Company Invoice option system will go to Purchase Invoice with all required details. From here you can create Purchase Invoice and Submit it.
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Both Sales and Purchase Invoice documents are having inter document reference which you can see in Inter Company Invoice Reference field.
Hope this will help you.