Securing sites

Can someone help with some security issues?

I want to...

1. Allow specific users access to functionality within a site (seems to be working fine - even though it only greys out the I want to... workflows that are denied.)

2. Allow specific users access to entire sites - This is not working so well. If I deny permissions on the site to a user, the url still takes them to the site, but then it just craps out before displaying anything, with an Initialization error.

3. Minimize the sites users can see in the Launch dialog box (setup through viewer.setting.xml) - the permissions set in Geocortex don't modify this

Am I missing something?  Is there a fairly easy way to fix these problems through Geocortex?

Any help?

Thanks in advance!

Paul