Haha you bunch of nerds!
Play the notes in live! Makes so f****ing much difference to your music!
Crytek has the right idea, play it in then correct where you want!
It’s the one thing I love so much about trackers: you can sit down, take your time
to figure out EXACTLY what your melody should sound like, then put the right notes
on the right places by hand for getting that perfect atmospere, recreating anything that
goes on in your mind, without having to worry about lack of playing/composing skills,
because EVERYBODY van play a tracker and you nevvah need to worry about having to
re-re-re-re-re-record your stuff.
It makes no fukking difference, except it takes longer. But you shouldn’t rush art anyway.
Even though I have a midi-keyboard hooked up, I mostly step-sequence my stuff using the qwerty-keyboard. It is (unfortunately I guess) the fastest way for me to get the job done without errors. 
I guess the midi-way works with basslines, leads and other monophonic lines, but I don’t like the way chords are entered into Renoise, as I in most cases prefer that the lowest notes is to the most left, and so on… instead of which key I hit first.
^^^^^
70% step-by-step
20% recording with a midi-keyboard and edit later
10% record with a midi-keyboard to wav and play the sample.
I enter all notes on a keyboard when creating melodies and such.
I notice some people don’t really make melodies and just kind of cut and paste a bunch of samples around. Using the keyboard for that is fine. When you are actually playing various notes I personally find a keyboard in my opinion is much easier.
Sitting with my computer keyboard and running my fingers across it trying to come up with ideas doesn’t sound overly sexy.