Recently bolnagri map in xkeyboard was updated to support additional characters for Marathi (ऱ, ळ ). Most recent distributions like Ubuntu 12.10, Debian Wheezy/Sid should have the updated keymap.
If looking to use Bolnagri for Marathi on older release, then follow these steps (need to be a super user to modify keymap file).
1) Replace /usr/share/X11/xkb/symbols/in with one available here.
2) Or patch /usr/share/X11/xkb/symbols/in with the changes here.
or manually edit symbols/in to make following changes to add (ऱ, ळ )
To access them use AltGr (RightAlt or chosen 3rd level key).
ऱ – AltGr+R
ळ – AltGr+L