I have 4 custom donation fields and they are appearing on my donation page but they are not appearing in the same order as in the custom fields section. I've tried dragging them into different orders but the order will not change.
I have 1 text field and 3 MC - the text one needs to be first if that makes it any easier to modify in liquid.
As Claire indicated below, the custom donation fields automatically appear in the order they were created or updated on new donation pages.
Additionally, by editing a donation page template, you can completely modify this process - by removing the code that pulls in all existing custom donation fields and inserting code to request specific fields in a specific order. The Requesting custom donation fields on a donation page HOWTO describes this process in detail.
Complete and current information on how to use NationBuilder is available in the documentation section.