Need help understanding servo operations


I have a servo MR-E-200A from Mitsubishi electronics. The unit has an amplifier and a position control unit FX-10GM. Here is the manual for the unit.

Goal: To control the servo using computer UI and the servo encoder's feedbacks.
I'm hoping that someone could help with clarifying a section of the manual.
The manual mentions general purpose inputs (X000-X003) and outputs (Y000-Y0007). Section 2 (p.33-45) describes the I/O. After reading through the manual several times, I still don't understand exactly how the pins are used and how to set them up. For example, in section 2.6.3, the instruction for Parameter No.56 said to set the input declarations to "1" or "3" and general purpose input can be used. What does it mean by setting and how?

Any hint or guidance would be appreciated!

Please note that I'm a self-taught electronic hobbyist and the projects I have done so far are Arduino related. This is a big step up for me so don't be too harsh in your response.

Thanks in advance!
I can't help answer your question, but want to congratulate you for your 'rare' ability to clearly communicate in your introductory couple of sentences: what devices you are working with, links to the manuals and clear definition of what you are trying to achieve and where you're stuck. That is SOOOOO rare in forum queries that yours stands out as explemary, to the extent that I am compelled "like" it for its clarity of content. Would that other forum participants had your ability to clarify their situations.