If you're already used to using the Project Sicario Builder to build merged mods for your game then PSM should seem very familiar! PSM is (to oversimplify) the "brains" of Project Sicario reworked to run locally on your PC.

That doesn't mean you can't use both though! If you already have a merged mod built using the Project Sicario Builder in your mods folder then PSM should automatically detect and rebuild it for inclusion in your PSM-merged mod. 

More importantly, if you want to use any of the patches available on the Project Sicario Builder app, you still can as well. Open the app and choose your patches as usual, but rather than clicking Start Build, click the new Save Preset button. You can then download a super-lightweight preset file that contains all the patches you chose as well as any parameters you set in the app. Install that preset file (it will be a '.dtp' file) into your mods folder (with Vortex, or manually) and when PSM runs next, it will include all of the patches in the preset file in the final merged mod.