You can use different ways to enter pitch [0].
A common way is to use the "octave.pitch" format, such as 08.04, where 08 is the central octave (if I remember correctly) and 04 is the note E. It's common to use a score generator such as PythonScore [1, 2], and some people (myself included) like to use a regular programming language to generate the scores. I've used Common Lisp, Tcl, and Python in the past. Csound has a few frontends [3] that people may like.
AFAIK, Csound can read notes from a MIDI keyboard as well.[0] http://www.csounds.com/manual/html/PitchTop.html
[1] http://jacobjoaquin.github.io/csd/pysco.html
[2] http://write.flossmanuals.net/csound/methods-of-writing-csou...
[3] https://csound.com/frontends.html
EDIT: remove some repetition
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