Do I need to nominate the boot disk in a new multiple disk system?

I recently had an ultimately unsolved problem with an existing Win 10 computer when trying to install & use an extra hard drive. I could see the extra drive and could use it normally but only for around a half dozen cold boots of the system. The system would then fail to boot until I removed the additional drive. I asked the question of the forum how this was so & was told to try different sata connections on the motherboard. This advice did not rectify the problem so I had no option but to permanently remove the second drive.

I now I plan to setup a new gaming computer that I am yet to install Win 10 on & suspect I may have the same problem with the intended SSD & HDD setup, because I suspect that with a dual disk setup the Win 10 system might need need to know which disk to boot from, which in this case I want to be the SSD. I say this because my experience with Linux dual disk systems is that they need to have the boot disk flagged during setup.

I'm still unsure if the problem with the above mentioned first Win 10 system was a boot issue or if it was a activation problem due to Microsoft noting a change in the hardware setup of the extra hard drive.

Could I please have your thoughts on this issue, as it might affect my proposed gaming system?
Thanks.

I would put ONE drive in it--the intended system boot disk. Install Windows 10 on it and get it running to your satisfaction and activate Windows.

Then install the other disk and do as you wish with it.