This question is about Installatron, but I assume Fantastico works under the same principle. How well does it handle modifications to a software package that it's trying to upgrade?
For example, let's say you install phpBB with Installatron, and then proceed to change the layout to match the rest of your site. And then you add a security question/answer in phpBB's user registration form as an anti-bot measure. What happens when you install an upgrade through Installatron? Does it wipe out all of your changes?
Installatron makes every effort to perform all upgrades in the cleanest, most risk-free way possible. However, there is always risk involved in upgrading a working application, no matter what method is used to execute the upgrade. Installatron has the ability to create a backup and rollback any upgrade, making it easy to restore the prior working version, with all modifications intact. You can even select individual files to restore.
In respect to phpBB theme modifications, it's important the modifications are forked to a non-default theme, since the default phpBB theme files are often updated by phpBB between versions. Forked themes will not be affected by upgrading.
phpBB also has a "custom profile fields" system that enables custom fields to be added to the registration screen as well as other screens. Custom fields created by this system will not be affected by upgrading.
Generally speaking, modifications should always be preserved as long as internal application files were not edited to achieve the mod. This caveat applies to manual upgrades as well as automatic upgrades. Whenever possible it's better to use a plugin system, templating system or advanced features to achieve the same effect.
I've never actually tried any upgrades through either of those installers for personal use but if the changes you made were to the physical files, AND if the upgrade requires you to replace those files then those changes will be wiped out but if the changes were in the database such as with the "custom profile fields" as mentioned above - they won't be touched because usually just the major parts of the databases are upgraded and all custom stuff are left untouched.
but just in case you should always have a backup of your physical files and database just in case anything goes wrong.