Oop's never mind I have found the answer by searching correctly this time.
Just uploaded a htaccess file to each sub folder I dont want re-written and its all cool.

Thanks very much
Chris

Add this to your .htacces rules:

RewriteCond %{REQUEST_URI} !^/dirname/.*

Where dirname is the name of the folder you want to be able to access without silverstripe interfering with that.

But I think you do not need that, because the .htacces will only interfere if you are accessing yourmaindomain.com/dirname, not if you acces yoursecondarydomain.com, even though it is in a subfolder of yourmaindomain.

This has been asked several times already.
The simplest solution (in my opinion) is to put an .htaccess into the subdomain folder (since that .htaccess file will take precedence over the one in the root folder). There you would typically turn rewriting off, or define your own rewrite rules for the subdomain. To disable rewriting, put the following in your .htaccess (for the subdomain)

Hi
I am having a problem with rewriting urls.

I want
http://www.domainname.com/forums/member.php?u=788
to be redirected to
http://www.domainname.com/

The prob is that "?u=788" remains in the url ie it looks like this
http://www.domainname.com/?u=788

I want to have "?u=788" removed.

I tried
RewriteCond %{QUERY_STRING} .
RewriteRule ^(.*)$ /$1? [R=301,L]

but it redirects to http://www.domainname.com/sapphire/main.php

I tried
RewriteCond %{QUERY_STRING} .
RewriteRule ^(.*)$ http://%{HTTP_HOST}%{REQUEST_URI}/$1? [R=301,L]

but it still redirects to http://www.domainname.com/sapphire/main.php

I tried

RewriteCond %{QUERY_STRING} .
RewriteRule ^(.*)$ http://www.domainname.com/$1? [R=301,L]

It worked but I don't want to explicitly indicate the domain name since I'll be testing it on a dev test server and then to a staging server which means the domain names would vary.

Any ideas how to solve this?

Thanks in advance!