Each mod is completely independent from the other mods and will not affect the default install of Fallout 2. Each mod can be run from its own shortcut in the start menu and will have their own set up savegames and settings.
Though you can only manage a settlement while in that settlement. This tutorial will cover how to configure multiple mods so that more than one can be installed at the same time without effecting each other. Now you view statistics, manage settlers, tasks, and settings.
Now you would go to a terminal and simply load your management holotape.
This makes helping your people so much easier and fool-proof, instead of running around trying to track all twenty of your settlers to make sure they are working. Settlement Management Software actually adds in a software for terminals that helps you control your settlement better! It adds control and significantly more than just barebones like food, water, defense, etc.