'the config detector looks in the wrong place to find mt-xmlrpc.cgi.'
Where does Windows Live Writer end up looking? This should all work right out of the box.
Though to solve your problem you can try the following:
Edit your wlwmanifest.xml file to have the following line in the options node:
<fileUploadNameFormat>path/to/where/you/want/your/uploaded/file/to/go/{FileName}</fileUploadNameFormat>
You can also use the following tokens to help you in your quest to place your files:
{Randomizer} -- You will need this if they are uploaded to the same folder and the names can conflict
{FileExtension}
{AsciiFileName}
{WindowsLiveWriter}
{AsciiFileNameWithoutExtension}
-Brandon Turner [MSFT]