I've just started digging through what I have and I have found one very recent invoice that I did not give permission for them to do.

I recommend having a handyman write you an invoice and fixing the problems.

Are all my invoices uploaded to my owner portal?

It becomes a challenge to keep all the funds, invoices, etc separate.

I would send them the invoice.

The reconciliation should be very accurate as the lease should also allow for the tenant the right to audit landlord's records including seeing copies of actual invoices paid.  

Are all my invoices uploaded to my owner portal?

For example, the best ways to construct and organize invoices for customer orders, how to file and organize those invoices, keeping track of "the books," such as asset and liabilities each month, and ways to organize the parts of the business that aren't the employees or physical inventory.Attempting to sum this into a "google-able" search has proven to be somewhat difficult, so I would appreciate your input.Thank you,

Are they transparent with their records (lease agreements, vendor invoices, etc.)?

Submit copies of all invoices and deduct from deposit.