If you have already configured Windows Live Writer with one of your Blog and want to configure your another blog also (something like configuring multiple accounts in your MS Outlook). I would say yes you can do it.
Steps are as under:
1. Select the Menu Weblog-->Add Weblog Account.. as shown in the picture
2. You will be prompted with the Choose Blog Type screen, select the appropriate option, I will be configuring my GeeksWithBlogs.Net blog (as I already have configured my Live Spaces blog).
3. Provide the Homepage URL and the Login information
4. Select the Provider (since GeeksWithBlogs.Net is not in the list I selected Custom (Metaweblog API)) and provided the Remote posting URL
5. Whew! that's it my blog configuration is complete. Just give your newly configured weblog a unique name, so that you can identify your different blog profiles in the Live Writer application.
Now you can select the weblog you want to work with from the Weblog Menu.
You can find more details about Windows Live Writer here.