I just wasted a bunch of time re-figuring this out b/c I had forgotten, so here is how you do it.
1. Get your web template name
This will give you the full name of your custom web template, which will be {[Template Feature GUID]}#[TemplateName]}
2. Create the site collection with powershell:
New-SPSite -url [Your URL] -
ownerAlias [Site Collection Admin Doman\Username] -Template {Web Template Name}