I would check that both drives are backed up and then install the OS with your normal setup intact and all drives connected. This lets the scripts see all your apps and in case you store photos or other system / user files on the other drives, any migration steps can run on that data.
All Apple installs are now archive and upgrade where the installer runs pre-install checks, pre-install scripts, makes a new system and then runs migration and post install cleanup scripts to move all your settings to the new system.
The APFS conversion is only for SSD exclusive boot system drives and nothing else converts automatically for 10.13.0 release. Fusion drives and HDD stay on HFS+ for the initial fall 2017 builds of High Sierra.
If you’re not sure you’re ready for this full install, consider installing onto an external drive and testing.