You should put the temp dir on the fastest HDD or even SSD if available. Also the swap partition or a swap file should be on the fastest drive.
You can also put the ~/.cache folder on the SSD if your home folder is on a slower drive. Read up on the use of links in Linux. It is even possible to put the calibre database and/or the format files on the SSD using links.
If your computer has plenty of RAM (>16GB) then you can even place the temp folder in RAM for the ultimate in fast drive. Linux has great support for this using tmpfs.
https://www.linux.com/learn/intro-to...ng-linux-links