Hey,
Unfortunately, I also do not know how to get what you want using aoctool. However, given that no one else has replied so far, I thought you might be interested in alternative ways...
As I just tried to solve a similar problem, I came across these two solution, which both work fine for carrying out an ACOVA as you described: 1. There is a tool on matlabcentral fileexchange, which I found very useful and easy to use: https://de.mathworks.com/matlabcentral/fileexchange/27014-mancovan
2. Brani Vidakovic gives code examples in the book "Engineering Biostatistics: An Introduction using MATLAB and WinBUGS". I think, Example 14.8. describes almost exactly what you want, so you can just re-program what is shown in the book.
Best, Matthias
Best Answer