When I create a custom link in my main menu, it automatically puts it at the bottom and I have no control over its order. Is there a way to re-arrange it?

For instance...I have a link to my vbulletin forums, but it's at the very bottom. How can I put it under my "Home" link instead?

try search for imenu or multi menu modules

or add this links for vbulletin forums by edit the main menu from template control panel

but fisrt you have to clone the default template because you can not edit the default template

1- go to admin panel
2- go to template
3- clone default template
4- edit your main menu template from system template

thats all

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if u would like to reorder the main menu you have to set the order of modules from modules admin control panel

The main menu is ordered like this:

"Home" link
Module link1
Module link2
Module link3
etc.

You can edit the template to put in a custom link like this:
<-- here
"Home" link
<-- here
Module link1
Module link2
Module link3
etc.
<-- here

Follow the procedure by meme