On a shared server I am forced to manage document roots of domains from cpanel which is buggy and consumes lots of time. So I redirected all domains to one directory lets say
if I understand your question correctly, you should be able to do it by using the flag PT (Passthru), which causes the rewrite target to be passed back to the URL mapping engine:
RewriteCond %{HTTP_HOST} ^sd1.(domain1|domain2).com [NC]
RewriteCond %{REQUEST_URI} !^/sd1/.*
RewriteRule ^(.*) sd1/$1 [PT,L]
Hope it helps.