That is odd, on my Debian "wheezy" system, the debian packaged guile is a symbolic link /usr/bin/guile to
/etc/alternatives/guile, which in turn is a symbolic link to /usr/bin/guile-2.0 . What returns from the command "which guile" on your system ?
The method I have tended to use, which may not be the ideal way, but works for my purposes is
to create a dir, /usr/local/guile2 and then
make && make install
I like this method, as when further releases come out, for example 2.0.12, I can simply create
another dir, for example, /usr/local/guile2012
I have geiser with emacs installed, so in my .emacs I have