Carlos,
I don't think that there is a way for you to put remarks into a running or start-up config anywhere you want to. If you want to put remarks in a stored config on a tftp server you can prepend them with "! or #" and the lines will be ignored when copied to a running router.
In ACL's for example you can put remarks in them explaining, in the running and startup configurations what each line does.
7600#sh run | be access-list
access-list 100 permit ip any any
access-list 100 remark permit everything to everywhere.
Hope this helps,
Don