If you look at your list of custom fields in
Preferences, you'll see they're grouped by field type. I'm not sure (because I don't use it anymore), but this may also determine how they are presented in the special
customsection of the default skin. Regardless of what order they're in, there's no way to change it. The only way to control the placement of a custom field is to explicitly define in somewhere outside
customsection. Once you have done that, it will appear there and not in
customsection.
My recommendation is to replace the custom section with a regular one, where all the custom fields are explicitly defined. Once you are satisfied that has been done correctly, then you can change their order or move them to other locations in the skin. My
Theatre View Skin illustrates the result. The top section of the skin (beside the poster) uses a mix of standard and custom fields presented in a logical order. Additional custom fields are left in another section (below the file info). This section was originally my replacement for
customsection.