Slot #2 for M.2s usually aren't as good as slot #1 on most motherboards, but the performance difference is somewhat minimal and somewhat likely to be non-noticeable, assuming you aren't picky about your numbers. It will function just fine in slot #2 while leaving #1 unoccupied.
However, if you only have one device using a SATA connection (the HDD), I'd still recommend using the M.2 in slot #1 as it is still a bit faster at the end of the day. The motherboard you chose comes with 6 SATA ports, so you'd still end up with 4 functioning ports to use for drives or any other devices (refer to the manual to see which ports specifically become disabled).
Also, do you already have the HDD in your possession, or is a planned purchase? If you don't currently own one, I'd suggest getting one with a SATA 3 6Gb/s connection, which your mobo has, instead of a 3Gb/s. It'll give ya better performance and you wont have to worry about potential compatibility issues.