A nice soluntion is make dynamic Enviroment vars
# SetEnv MAGE_MODE "developer" # Only for debug
SetEnv MAGE_RUN_TYPE "website"
SetEnvIf Host "^([a-z]+)?\.?([a-z]+)\.?([a-z]+)\.?([a-z]+)\.?([a-z]+)$" MAGE_RUN_CODE=$1$2$3$4$5
use if domain is mydomain.com make a website called mydomaincom
if domain is shop.mydomain.com make a website called shopmydomaincom
make a phpinfo.php in your webroot directory and see if enviroment work if magento tu instalation host.
