I'm using GoDaddy with several websites as alias's to my main site.

I want to do a 301 redirect from ccwtech.com to www.ccwtech.com without causing other alias (subdirectory sites) to have issues.

I tried this code, but it causes the alias sites to be shown wrong.

Options +FollowSymlinks
RewriteEngine ON
RewriteCond %{HTTP_HOST} ^ccwtech.com [NC]
RewriteRule ^(.*)$ http://www.ccwtech.com/$1 [R=301,NC]

(if GoDaddy Alias's isn't familiar to you, it allows you to have a seperate url (like www.lonepeakvet.com and it really is www.ccwtech.com/lonepeak [for example].

When I use that redirect to get non-www to www on my main site, it then shows www.lonepeakvet.com as www.ccwtech.com/lonepeakvet [example only].

Any help?

IF you are still not able to redirect you need to talk with Godady's executive it might have problems because of shared hosting. Also add canonical URL to the page which you want to redirect to original one so Google will index one of them specified with canonical.