Advice on indexing a search table, should I or shouldn't I? I'm making a search page on my website and I have 3 different areas that need to be searchable. 

Should I make an index table for each using MyISAM engine. Or should I just put the extra data inside of the previous tables using InnoDB?


MyISAM (separated index table)


benefits 


faster loading/search

cons 


need to use CRON jobs to update it daily, same data in 2 places


InnoDB (all data in same table)


benefits 


data all in one place, easier to maintain, instant updating

cons 


possibly slower loading times




Does anybody have any advice on this?
You should use only InnoDB.  Period, Full Stop.

MyISAM is going away.  MyISAM is rarely faster than InnoDB.

With 5.6, you get FULLTEXT indexing in InnoDB.  With 5.7, you get SPATIAL indexing.  So, upgrade if you need to.