When you install MOSS (not evaluation copy) part of that process is creating a Shared Service Provider. This is essentially a set of services like User Profile store, Search, BDC, MySites etc… These services can be consumed from one or more SharePoint Web Applications (and other apps outside of SharePoint if you like).
One of the services that an SSP provides is details on where users MySites are located. This is because if you have, for example, multiple Portals then you usually only want a person to have one MySite. So by having multiple web applications consuming from one SSP you can achieve this.
However, by default when you create an SSP the MySite location is set to be under that SSP. I think an example will help here…
Your organisational portal site is on http://OrgsIntranet
Your SSP must be on another URL domain or port so let say... SSP1 is on http://OrgsIntranet:12345
What this will mean, by default, is that your users MySites are at http://OrgsIntranet:12345/personal/<username>
As you can probably imagine, this is not ideal for all organizations. In fact for most organizations that will only ever have one main portal this is not ideal.
The reason we host MySites on another web application is so that no matter what site you are on, when you hit the "mysite" link at the top of the page, it will take you to the right place and that place is not dependant on any individual portal.
In an ideal world you would have an address like http://my or http://mysites as a DNS name for your SSP … so that the address makes sense and you could run it on port 80 like everything else. It makes the URL look nicer I guess.
Anyway! So for orgs with only one main portal they might want their urls to look something like:
Org Main portal: http://OrgsIntranet
MySites : http://OrgsIntranet/personal/<user name>
So how do you go about configuring this? …
I am assuming you have your intranet/portal at http://OrgsIntranet and the mysites location is currently at http://OrgsIntranet:12345/personal/<username>
Done! Now when your users click on the "mysite" link their MySite will be created in the right place.
NOTE: if you do this after some mysites have been created then you will have to move them using STSADM to the new location. Otherwise a new mysite will be created for them.