I think what you are asking is "How do I manage anonymous access for SharePoint / WSS sites?".
This article should get you started.
FAQ - How do I enable anonymous access
?
Enable anonymous access for a web
application from the Central Admin.
Central Admin Home Page > Application
Management > Authentication Providers
select the Membership Provider (authentication.aspx) and enable
anonymous access from the next page.
You don't have to do anything on the
IIS Manager ... enabling it from the
Central Admin page will also enable it
on IIS.
Explicitly turn it on for the sites
you want to be accessed anonymously.
Browse to the site, click Site
Settings > Advanced Permissions >
Settings >Anonymous Access
(setanon.aspx) and turn on anonymous
access for the site.
From Mark Harrisons blog http://old.markharrison.co.uk/blog/2006/06/moss-2007-enable-anonymous_12.htm
Based on your follow up comment I believe you are asking if you can manage anonymous access when logged in to your default zone which only supports Windows Authentication. For some reason MSFT decided to disable the page controls on (_layouts/setanon.aspx) when access the site collection using a Web Application that has anonymous access turned off.
Since anonymous access is just another setting for the Webs there is no reason you cannot build your own web page to manage those settings. This article can help get you started. Granted this article discusses building an STSADM extension which will NOT help you manage your site via Web Browser, it does have the code you would need to have inside your custom page.
You should NOT need a special FBA account to manage the anonymous access. You can management it with any account that has proper permissions in your site collection.