Multisite installation into a subdirectory of a multisite cpanel instal

Okay - I know the first rule of mulitisite is to install it into the top level directory of your server... ie /public_html/ for the typical cpanel installation.

However, my client wants a second installation of multisite done this way:

/home/account/public_html/seconddomain.com/

he already has one at:

/home/account/public_html/ with the first domain.

He has a reason for this, and it is not particularly valid - other than he wants to split up the number of domains per installation. Everything works fine with the second installation until we go to use domain mapping. During the installation the network code that was provided for the .htaccess as identical for the second install when compared to the first install. I knew this was going to cause issues.

Is there a written step-by-step instruction on how to do this weird configuration? I assume the biggest issue is the .htaccess file.

Any advice or suggestions would be appreciated. I searched this topic and I am sure others have asked about it. Could not find anything here on it.