What are the software issues with installing a 2nd SSD on my mac mini (Late 2012?)

Hi Everyone,
I've just bought a brand new Mac Mini server - 2.6GHz, with a 256GB SSD.
I have also bought a 512GB SSD from Crucial, along with a Dual Drive Install Kit from OWC, and will probably be installing it myself.
I've read a lot of info on various forums/websites that is a little concerning.....regarding data loss when you reboot the Mac having installed the new SSD (not sure if this just applies to adding the SSD to a system that contains a 'normal' HDD.....)
If I'm going to have 2 SSDs in my system, I guess there are 2 questions:
1. Can I just add the new 512GB SSD without any reboot issues
2. Is it important to keep the system SSD physically where it is, i.e. at the bottom of the Mac (and plugged into the same connection on the logicboard?)
Thanks in advance for any help!

Thank you so much John and woodmeister50, most helpful
Just one more thing - the crucial drive came with a data transfer cable (SATA to USB) - I haven't got my dual drive install kit through the post yet...so do you foresee any problems with me installing the software that I will be using on the 512GB drive, in preparation for it being internally installed - is that possible to do with this cable?
Thanks again people!

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