>if money enters the company account there must be documents.
That would be via company bank statements. No invoicing. In some cases, Apple sends out documents related to taxes.
Financial reports are available via iTunes Connect. Payments are electronic.
>does apple invoice my company their fees?
Wrong term. As for 'fees', remember the 70/30* is a revenue split, where Apple takes 30% of the transacted revenue, not 30% of your 100% - the 70% (more like a royalty) from the transaction is your '100%' (taxable amount/your burden where applies) and no fees are taken from it. Note the absence of your use of 'fees' in your Developer Program Agreement. https://developer.apple.com/terms/
Your 'fee' is the annual USD$99 for the Developer Program Account. That invoice is found in the online Apple Store account tied to the main Apple ID on the dev account.
*May vary where VAT etc. applies.