The advice you received from i7Baby is absolutely correct. This is NOT a debatable issue. There is nothing, absolutely nothing, to be gained by having your HDD (which will be serving as a secondary drive following the installation of the OS) installed during your fresh-install of the OS onto your SSD.
Admittedly there is little likelihood that any problems will arise even if the HDD is installed during the install of the OS but !@*# happens as we all know when working with PCs. The prudent course of action is to disconnect the HDD from the system and then install the OS.
The SSD should be connected to your motherboard's first SATA connector which will be designated either SATA0 or SATA1. The HDD should be connected to a SATA connector designated either SATA1 or SATA2.
I assume you're going to use the HDD as a secondary storage/backup device. Avoid making any major changes, e.g., formatting, until you ensure the installed OS on the SSD is bootable and functions without any problems. Then you can do whatever you want with your HDD.