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12) Click "Contrasts & F-tests" tab. 

13) Create contrasts:

To compare the means of two samples, set both Contrasts and F-tests to 1. Make sure the box next to C1 is selected (it should be yellow). Select the F1 box. 

If you have more than one cariable, create a separate F contrast for each one. Additionally, create an all-effects F contrast (e.g., for 3 EV's, 1 0 0/0 1 0/0 0 1). Here is an example with group + 3 covariates - F5 is the "all-effects" F contrast (we can use this to determine fit of the model).

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11) Save the file

Under the GLM Setup window click Save, navigate to the directory with the files, and choose a descriptive name ("des_2sample" for example; you can use des_[folder name] using the name of the design folder). You can ignore the warning.

This will save a number of files, as in the example below (where "des" was chosen as the name). These files are used as input to several of the following procedures.