Setting up to type Unicode Nepali in Ubuntu is easy (just add Keyboard Indicator applet and add Nepali Layout). For more, follow this article in Ubuntu Nepali wiki. However there are few glitches.
Incomplete keyboard layout
The Nepali Romanized Keyboard layout shipped with Ubuntu (located at /usr/share/X11/xkb/symbols/np) is incomplete. The definition for the whole upper row (1-0 keys) are missing. Also, more importantly, zero-width joiner (ZWJ) and zero-width non-joiner (ZWNJ) characters are wrongly defined (ref: standard layout map).
You can find the working version here: http://www.nepalinux.org/input/ne. So lets, fix it. Fire up your terminal
$ cd /usr/share/X11/xkb/symbols/
$ sudo mv np np.bak
$ sudo wget http://www.nepalinux.org/input/ne -O np
The devanagari fonts included in the standard Ubuntu installation has few Nepali specific glyphs missing. Most notably, 'pareli ra' or 'samyukta ra' (whatever it is called, the one you use in the word 'paryo').
Well, the fix is to install a font file which has this glyph. My recommendation is Lohit Nepali, available at http://nepalinux.org/fonts/. At terminal,
Now if you want a specific font file (say, Kalimati) to be used as default devanagari font file, follow the following procedure.
$ cd /usr/share/fonts/truetype
$ sudo wget http://nepalinux.org/fonts/Lohit-Nepali.ttf
$ sudo fc-cache -fv
Create a file in /etc/fonts/conf.avail/
and paste the following content
$ sudo gedit /etc/fonts/conf.avail/64-ttf-nepali.conf
Now, create a symbolic link to it in /etc/fonts/conf.d/
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
You might have to restart X to see the changes.
$ sudo ln -s /etc/fonts/conf.avail/64-ttf-nepali.conf /etc/fonts/conf.d/64-ttf-nepali.conf