Hi Darryl,
If you need to adjust core functionality I would create a completely separate module so that future upgrades will be easy and painless. - eg. for creating a custom registration form.
If however you wish to customise an existing module such as the links module, there is no reason why you can't copy this modules code and rename it to your own module so that this module is also completely separate. - This way in any future upgrades, a new version of the links module will not wipe over your own version of the links module.
You may also want to check out this module (I haven't used it so I can't comment on it's functionality):
User Attributes - It allows you to create your own forms and choose your own registration options:
http://dnn310.ucanuse.com/PortalMod...fault.aspxI would also check out this post which discussed
http://www.dnncreative.com/Forum/ta...fault.aspx">customising the DNN registration module
the principles outlined here will also apply for customising the login module.