I have been installing with multiple drives for awhile now, and I just make sure I am aware of the partition size allocated for /root and /home and a swap in between which makes it very noticeable to me, which is on my first drive. My second drive which is a very large drive with two very two large partitions for my music other media on the second drive. Just make sure during the install to take your time and avoid distractions. Of course there is nothing wrong with being extra careful and disconnecting the second hard drive if it easily assessable, and if you are comfortable doing that.