Re 1) your command is nearly correct, but you actually have 2 group-types (group and gender), so 
shapeAnalysisMANCOVA ./designfile.csv --infileColumn 8 --numGroupTypes 2 --numIndependent 6 --columnGroupTypes 0,1 --columnIndependent 2,3,4,5,6,7 

Now, how does shapeAnalysisMANCOA know which one of the group columns to use for testing. By default it will use the first column (index 0), which is why you do not need to specify it in the above example. So the above call is the same as this one:
shapeAnalysisMANCOVA ./designfile.csv --infileColumn 8 --numGroupTypes 2 --numIndependent 6 --columnGroupTypes 0,1 --columnIndependent 2,3,4,5,6,7 --testColumn 0

Now let's assume you want to test for gender then you would call: 

shapeAnalysisMANCOVA ./designfile.csv --infileColumn 8 --numGroupTypes 2 --numIndependent 6 --columnGroupTypes 0,1 --columnIndependent 2,3,4,5,6,7 --testColumn 1