There are multiple options for coupling MATLAB and Eclipse. You can either use "system" function in MATLAB to call Eclipse for a single run, or use "eval" to run Eclipse through command window, If you have multiple runs at the same time (parallel simulation).
For Eclipse (E100, frontsim or E300) you can run their .data associated files from Matlab using the following function: !eclrun.exe -v your_version e300 file.
You can also develop some scripts for generating automatically your data files according to your optimization problem (such as well placement, history matching ...), then you can run them directly from Matlab and extract their results.