You have 3 deposits every month for rent, a mortgage to pay, contractor invoices for maintenance here and there, and utilities once a quarter.

I'm wondering if anyone has recommendations for electronic receipt / invoice storage compatible with Mac? 

For labor we were thinking of using our business checking account to wire money or even use Venmo through our business account.For things such as furnace, flooring, paint, lighting, etc. we were thinking of using our business credit card, and buying all those things ourselves.We'd keep a copy of all invoices for labor, and receipts for purchases for tax purposes.Is there any advice or anything we should do differently?

You don't want to get stuck in an audit with your pants down.If your movers are billing for cleanup, have them break down the costs on an itemized invoice so that your business expenses are clearly defined.Good luck!

The tenant has the invoice from the plumber and will send me a copy.

You will need to make a naming standard for each invoice.

With the Quickbooks version I use (Simple Start) they don't allow automated invoicing however I believe with the essentials & Plus versions they do allow reoccurring invoicing but I've not seen it in action.  

Enter a maintenance request, assign a vendor, attach a fake invoice.

A good solution would be adding yourself as a service pro, and if you don't want certain invoices to be visible to the tenants, assign them to a service professional. 

(Well, I can manually accept a credit card payment, but I can't send recurring invoices and accept ACH payments, which is what we really need.)