By default a dedicated server reads values from a config named servertest.ini. I'm assuming that you already have a config. If not, create one.

If you have a control over the server config ini file (on your PCs you do, I don't know about 3rd party hostings), you can do the following:

1. Copy the config to the PC you run the game on. On windows the path will be C:\Users\<user>\Zomboid\Server\servertest.ini.
2. Launch the game and open Mod Manager: Server.
3. Choose the config you want to edit.
4. Add/remove mods and save it.
5. Optional. If you added mods with maps in the previous step, edit this config again in the vanilla editor (check this mod's description!).
6. Rename your config to servertest.ini if needed.
7a. If you run your server on the same PC, just start your dedicated server.
7b. If you run it on a different PC, copy your config and put it in the appropriate folder on that system.

Make sure that you have Mod Manager: Server version at least 1.1.0. You can find it in Mod Manager. Otherwise, it will thow an error.

Presets created in Mod Manager (hereinafter MM) are located in
C:\Users\<user>\Zomboid\Lua\saved_modlists.txt
Presets created in Mod Manager: Server (hereinafter MM:S) are located in
C:\Users\<user>\Zomboid\Lua\saved_modlists_server.txt

1. Create a preset in MM:S without any mods: load any config, select Disable All in the presets dropdown, and save. For this tutorial I called it ImportedPreset.
2. Open the MM:S presets file. At the bottom you will see this:
3. Open the MM presets file. Find the name of your preset. In this case it's called PresetToExport
4. Copy everything after : (colon) and insert in the MM:S preset after Mods=. Now it looks like this:
5. Save the MM:S presets file.
6. Restart the game.
7. Open MM:S and load your ImportedPreset.
MM:S will pickup Workshop IDs (for mods from the Workshop) and add them.
8. Save this preset. MM:S will add Workshop IDs to the presets file automatically.