1. Scanning the encounter forms/superbills into a document and sending them using a HIPAA compliant/encrypted email server is easiest, probably.
2. There is a lot of information/advice/debate on this forum about how to charge for your services. Do a search using the Search box, and you will see post after post about it. Percentage billing is common, but not always legal, and not the route I would take, as it just doesn't cover all that goes into what you do, usually. I would do a flat monthly rate, or a per hour rate. Only you can determine what that rate should be, based on what services you will provide. And whatever you think is a fair rate, you will probably be wrong, unless you factor not only the billing work into the cost, but ALL your overhead also for each account you may get. And you still might sell yourself short.
Take your current employer. Let's say they pay you $20 an hour right now. If you plan on doing everything you currently do for them when you have your billing company, that is your base pay/rate, and configure it from there. Factor in your overhead, and either go hourly, or figure out how many hours you will spend on the account, and come up with a monthly rate.
Things to consider:
1. Your employer will no longer be paying taxes, etc. for you as an employee, so that is saving them money. If they balk at your rate for any reason, you could gently mention this. As well as the fact that you are paying for all the overhead costs.
2. Because they are your current employer, you may be tempted to give them a lower rate, which is understandable. But you are trying to start/run a business, so don't get trapped into a situation where you aren't making any profit at all on that one account.