I am considering purchasing JMS for use with my sites. But I have one question: I have installed Joomla on my site using Fantastico. After I install JMS, can I continue to update the master site using Fantastico, or do I need to manually install Joomla in the master site, and no longer use Fantastico for updates?

Thanks in advance for your help!

I don't know the details concering the fantastico update but in case where you can not do it while JMS patches are uninstalled, you probably can just un-install the JMS patches before using the fantastico.

We always recommend to un-install the JMS patches before any update of joomla itself because we already had some files modified by joomla that restore orgiinal files and therefore remove patches installed by JMS.
To guarantee the consistency and avoid problem to login, we prefer to always recommend to un-install the JMS patches to restore a "native" joomla on which you can install the update.

So with fantastico, this should be the same.
I don't know if fantastico is doing other things.

JMS install the patch on the joomla file provided and it does not replace them with static one.
So you can always benefit of the joomla security fixes as JMS research in the source files some pattern to identify the peace of code that must be modified or enhanced.