That's exactly the reason I don't want to use it as well. It was working before the update yesterday. Based on comments, it looks like it has compatibility issues with BepInEx ConfigurationManager now.
The relevant comments I could find and information on the mod were all here: Nexus Mods Valheim Plus (install instructions are on the description tab). As an example, one mod I know requires the configurationmanager is Valheim - Quality of Life.
As for installing mods manually, I would typically add BepInEx with the instructions here to the Valheim folder. And I would drop any mod .dll into the plugin folder once that's added. One that requires server files as well is Any Portal, which would typically be simply manually downloading the .dll and dropping in the BepInEx/plugins folder on both the server and client.
I hope this is what you were asking for. If there was a way to simply enable starting with server_bepinex without valheimplus allowing for other mods added to the plugins folder, that would be fantastic.