You can enable it after the fact, but be very careful when doing so. I would strongly recommend backing up your website before installing any SEF component.
POSSIBLE PROBLEMS
If not done properly, activating SEFsh404SEF on an already established site can have the opposite effect of what you are trying to achieve. Why? Consider the points below:
- Your current URL structure is most likely already indexed by several search engines.
- Websites have probably linked to your pre-SEF URLs.
When you activate your SEF component it will change your URLs. If your SEF component doesn't map (redirect) visitors from the old URLs to the new ones you will lose SEO rank and get lots of 404 errors.
SEF components can be complicated (at least for me) and proper mapping (redirection) of old urls to new ones can be a pain.
Make sure you thoroughly research your SEF component before installing it. Sometimes links will be created differently to how you would expect. For instance, I believe that sh404SEF doesn't use menu structure to create the url. It instead uses the category structure to organise(Br.E) the way the URL is made (please correct me if I'm wrong).