There's no way for me to say without more information.
If you have different geoprocessing operations, why not have different models?...and if you needed to run them both unattended (like overnight), you can either set up individual scheduled tasks, or a single task task set up to launch your models, say via a batch file- as many different models as you need. You could even set up a task to launch a Python script controlling run of your models. It's up to you.