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Assuming you are talking about Classic Repository Based CAPS 6, all details can be found at: http://wikis.sun.com/download/attachments/38767325/JavaCAPS6+Application+Configuration.pdf.
Essentially - first you create (extract) the configuration, before you change it and import it. Note that it could be a good idea to remove any SJMQ configuration from the file before importing it - or explicitly set the authentication information in the file, since the existing user/pwd will not be properly generated. In addition if you use JMSJCA options in the Connectivity Map (such as redelivery) they will be superseded if you override the SJMQ information - and thus not work at all.
Sorry, spoke too soon - the PDF the link led to was too generic. Instead look at: http://wikis.sun.com/display/JavaCAPS/Application+Configuration+Lab.