How do we deal with waivers on a sales invoice? How do I create a paid sales invoice automatically from a sales order …ie after submitting the sales order?
You can try to use discounts on Sales Invoice
You may to customize to do this from Sales Order depending on which version of ERPNext you are using. You can however directly create a payment from the Sales Invoice by “Include payment” checkbox.
For waivers how do I generate reports from discounts? Waivers are given by the government and would like to send them an invoice at the end of the month
Your case is a quite local and vague? Please explore a bit, search this forum, read the docs and try stuff out. Then when you are stuck explain precisely what the problem is?
You need to do your homework first and inform us what you find out 
edi: Perhaps check in with the Health group List of module volunteers