In the Joomla CMS each module is placed to template specific position (see Administrator > Extensions > Module Manager / column Position. For graphical presentation see Administrator > Extensions > Template Manager, click on used template name and then click toolbar button Preview).
Starting with JotCache, ver.4.1+ module exclusions are simply implemented as a selection list of enabled template positions on the site :
On the form can be selected any frontend module position which is assigned and enabled in Module Manager.
Mark in your template only module positions which you like to be steady refreshed. When page is cached then all JotCache mark tags are stored with cached content. During recall of cached content the marked positions are replaced with module newest content.