Hi there @thomasbazoo!
Don here from Shopify.
You can see how easy it is to change your Shopify plan level here on our help site.
When you change your plan level, a new bill is then issued for the new rate, but any time already paid for would be prorated and converted to be used towards your new plan level so you never lose out!
I'm not fully sure I understand your next query here, but it sounds like you're asking about how and when transaction fees are applied for third-party gateways, which you can check out here.
Let me know if there was something else you wanted to know about in this regard.
Our plans, rates, and fees are set in their price and it would not be possible to negotiate these rates in any way.
Not to worry, as we have seen above, you can easily move up or down in plan level from month to month as your business needs dictate.
Would you still be setting up your store or looking to start out, or have you been selling a while already?