Does the PM mark-up contractor invoices, and if so, by how much?

One has sent higher invoices than usual recently after particularly messy guests.

However, they continue to send me an invoice for these reservations - which I am refusing to pay.  

They will not fund until I send pictures of the repair, a paid invoice from the company and a formal draw request.Both are fine, but just different trust levels.

Eventually, after sending default letters and invoices showing what the late fees and default interest rates were he began making payments sporadically.

Ours is a big help with late fee enforcement as the tenants invoices have late fees added to them as soon as they're late. 

From my understanding, as long as you keep the documentation you may be able to use an excel file with the expenses - tab for each property with the first as a compilation - and then attach all the corresponding docs to support the expenses - IE receipts/invoices for the legal fees, closing costs, etc. 

No tenant calls, and I'd only get invoiced for things happening at the property (everything taken care of promptly).Does anyone have experience with a setup like this?

Seasoning periods vary and it's not all that uncommon to find a lender that will allow 90 days, even NO seasoning if he can document the value add to the property (invoices, receipts, before/after pics, etc). 

As long as you have a detailed scope of work along with a contract, yes your contractor should be sending you a detailed invoice for any change orders.