I do not know what the goal is for fis.c or fismain.c. It seems to me that you want to have the data in FLD format stored in a two-dimensional matrix. You can do that if you parse the results obtained with the FldExporter.
However, if you want custom input vectors, you can have two matrices, one for inputs and the other for outputs. Then, you can easily create both matrices yourself using fuzzylite. You do not need the fis.c or fismain.c to do it for you, roughly, you can do it as follows.
for every input vector v: for every input variable i: i.setInputValue(v[i]); engine.process(); for every output variable o: w[o] = o.defuzzify();
where v is a row of the input matrix, w is a row of the output matrix.