I will gladly provide guidance to the best of my ability, but if something should go wrong don't get mad at me I don't really mind helping you with non-rclone stuff even if it off-topic, but as asdffdsa said - it's all at your own risk (even if I wouldn't say there is much risk). I am a bit of a hardware nerd so this stuff is very familiar to me.
#Crucial clone instrutions manual
You'd have to give me specifics on what motherboard model you have and what drive-model you bought for me to give you exact advice in this regards (I can look up the details in the manual for you). On a newer board it's likely all S-ATA3 - unless it's so new that you are talking about M.2 card-slots (in which case there are S-ATA and NVME variants of these). Older boards may have S-ATA 3GB/s as well as S-ATA 6GB/s interfaces and you wouldn't want to connect a new SSD to the older port. Depending on the age of the motherboard it is quite common to have a couple of high-performance ports using the latest standard and then maybe several more cheaper ones maybe a generation behind. The only important thing I would actually pay attention to is which ports on the motherboard are what standard (often color coded). This is not fixed to the physical connector and you can change it at will easily.
Which drive is then used to boot from later on is something can select in that boot priority in BIOS you mentioned.
It just needs access to both drives at the same time. To the best of knowledge it should matter very little if at all what ports you use to connect the new drive to do the cloning in.