There are different ways of doing it, which should be adapted to your application. This involves interacting with COM objects, both in Phreeqc and COMSOL. It's not MATLAB itself that can tell you how to interact with these software, but knowledge of them.
If you want to do it on high-level, then you should first learn how to build models for your specific case using keywords/commands for each program. Everything you do in the software while you are interacting with UI can be represented as sequence of keywords/commands, and you can probably find a way to get it in a textual way (usually it's called macro recording, but the name can differ). You can use this information to figure out how to create a model "programatically" using any programming language.
https://water.usgs.gov/water-resources/software/PHREEQC/documentation/phreeqc3-html/phreeqc3-3.htm#50593799_12744 Last section mentions COM capabilities of the software.
I am sure there are plenty of resources on COMSOL side of things on the internet if you just search.
