Should WPERP be installed along with the main website WordPress, or should I create a subdomain, install WordPress, and install WPERP on the subdomain by itself?
You are free to install the plugin anywhere that seem convenient to you. Installing on a sub domain will only allow to avoid plugin or theme conflicts.
If your site and WP ERP both going to have significant amount of users, then you can have a separate installation to balance the loads better.
On the main site, I will be using SSL. Will that cause any issues with WPERP? Is there documentation on best practice when setting up employee logins to track times, to keep them out of the rest of the WordPress install like themes and other plugins?
We have not received any issues about SSL till now.
All the user roles of WP ERP is built over the “Subscriber” role of WordPress. So the ERP users will only have access to their designated pages.
Only the admin will have access to the themes and plugins listing.