I have no experience with GMS, but if you are using windows you shall know about creating a batch file (a file that executes multiple exe files with the sequence you need). If you are using linux you should know about shell script files (they do the same for Ubuntu). If you are connecting c++ files to build a project use CMake. If you want to run an exe from your code see this link http://www.cplusplus.com/forum/general/4156/
I don't have much experience with C++, but I would suggest you to use Python for groundwater modelling. You can use the FLOPY package which is very convenient. Once you write the model input files (.nam and other files) with GMS then you can load the model and run with FLOPY (python). I am doing the same for my research. And yes with batch files you can also run the model but I have had great experiences with FLOPY (using python jupyter) so far.
But skills and expertise of Dr. Boudjéma Samraoui are Biology, Entomolog, Ecology, Bioinformatics and I don't find groundwater modeling (GMS) in his skills.
One thing you can do... If you save the native text documents while creating your model. then all the files will be saved in text document. then you can easily run modflow exe file with name in c++