Hello kdawes01,
Thank you for your question. Softaculous does not have access to the program itself once it is installed. It is just an installer or remover of the program. You can, however, have Softaculous check for updates or do automated backups when they come out. Are you asking about one of those options instead?
Using one of the articles linked above, you will be able to uncheck the option so that Softaculous will not upgrade or backup the files. Other than that, Softaculous has no access to the files or databases.
Kindest Regards,
Scott M
http://www.softaculous.com/docs/How_to_Remove_Installation_without_deleting_files
Make sure you have unchecked all the check box so that your files and database are not deleted.
Hope this helps !!