Precision of terminology is extremely important here -- and you're not very precise yet. Are you using ISAM as a generic term to mean indexed sequential file access, or are you referring specifically to IBM's ISAM implementation? The difference is that IBM no longer supports use of their ISAM implementation so you cannot code up JCL or COBOL to use IBM's ISAM implementation.
If you're referring to ISAM to mean a generic indexed sequential file access, you need to Google VSAM KSDS and find out how the JCL and COBOL statements are used with VSAM KSDS files.
IBM's web site also makes mention of Informix's C-ISAM which IBM does support -- but again that is not the IBM ISAM implementation. And I'm sure a Google search will find you plenty on C-ISAM as well.