If I understand your question, you are provisioning a site with a custom site definition (or OOB) and would like to activate some features once the site is provisioned.
You should staple your features to your site definition. Basically created a feature that associates your feature (by Guid) with your site definition (ie. STS#1).
You can control the order in which your features fire using this technique. Ideally you would create a custom site defnition that is more or less empty and then activate all of your features using the stapling functionality of SharePoint.
More here http://msdn.microsoft.com/en-us/library/ff648422.aspx
(FYI - 2010 has a site provisioning event receiver you could look into)