Hi Suzzane,
The plugin itself doesn’t allow you to create custom checkout pages for users. However, you can decide if a wholesale user needs to pay or not, so they can just submit an order (like a purchase order) without having to pay. You can also choose whether or not they are taxable and set up different tax rates for wholesale customers. You can also disable shipping calculations & coupons for wholesale customers as well. So, all those options will change the checkout process for wholesale customers.
Since there is a separate role for wholesale customers, you can create your own checkout page template and use some conditional statements to show different things to wholesale customers versus retail customers. Woocommerce is very flexible with their templates, and all you need to do is move a template to your theme’s woocommerce directory (with the appropriate subdirectories to match the woocommerce templates directory structure) and woocommerce will use your template instead of the built-in one.
You can also use the Role Based Payment/Shipping Methods plugin to choose different payment and shipping methods based on the user’s role:
http://www.woothemes.com/products/role-based-payment-shipping-methods/
I’m currently using that plugin for a client site we are developing and have create some simple payment gateways called “Quote” and “Purchase Order” that only appear for certain types of customers (based on roles).
As far as phone support goes, this company is just me for right now, so I don’t have any kind of full time support staff. However, I’m happy to set up a time to talk to you on the phone if you need some custom work done or support for a purchase. Most support is done via email and the support forums, though.