Manual Payment - a few questions

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We are setting up to sell uniforms online to a company's employees so they can purchase a new uniform whenever they need one, without having to wait for a PO from the company.  So far, so good, but the company has expressed interest in having the uniforms paid through a payroll deduction plan.  The best solution I have found so far is to set up the option of using manual payments, so that the employee places his order and then we can mark it paid once the company pays us using the business credit card.  I have a few questions about how this would work.


1. If i bill the company by sending a single manual invoice for the total due over a week's worth of orders, and the company pays with a credit card through that invoice, when i mark the individual orders as "paid", will the total sales report we run for that time period report for just the actual money taken in or will it report both, causing an erroneous report?  In other words, if we have four sales for a total of $100 on manual payment, and the company pays $100 by credit card on the invoice I create and send, will the sales report show $100 in total sales or will it show $200?


2. is there a way to create a payment invoice that will automatically mark the individual order invoices paid, or distribute funds to those invoices so they are marked paid?


3.  Is there a way to have manual payments be an option only for specific collections?  Preferably without having to code anything as we don't currently have anyone to code for us.


4.  Can a customer do partial payments, such as use a credit card to pay part and then manual payment for the remainder of the balance? (The company will be paying weekly with their card, and expect a lot of orders every week, so i'm not sure the app Split-Partial Payments, which allows for "sharing" payments, is the way to go because the company understandably doesn't want to deal with making many repeated payments all the time. I didn't see any better apps, though.)


Thank you in advance for any help.