I have not installed these packages from source, but normally there is a file called configure. I am guessing you want to choose where the package is installed to and I will explain how to do it in a sec.
Normally you do something like this:
The make install installs the package to the appropriate directories on your system. For example it may install the executable mldonkey file in /usr/bin or perhaps /usr/local/bin.
If you want to change where it is going to install to you can do this by passing information to the configure:
for information about what you can pass to configure type:
It seems that you are installing packages to you desktop for you root user. Are you running Xwindows from root? If so you should consider running it from a user account and install packages to a different directory.