Usually the cache only needs to be loaded once when the database is created. After the initial load, specific pages are either indexed manually or (if you have autoindexing enabled) they all are automatically indexed.
Because the MantaDB index database does not store duplicate entries it will not hurt to activate the Index Explorer Cache button again in the future (perhaps to pick up a web page you forgot to manually index). MantaDB will just add the pages in the cache that are not already in the database and ignore the rest.
The indexing of the Internet Explorer cache is started by selecting the Index Explorer Cache button in the Tools menu of the configuration dialog box.
WARNING: The cache indexing procedure can take some time (10-15 min) especially on slower machines or those with a large cache. Your computer will be very busy during the indexing process and you will not be able to get a lot of use out of it for other things during that time. Be prepared to leave it alone while MantaDB gets on with the indexing.