Hi Devon,

First, your predictors should be matrices not cell arrays. For a 3 level factor, you'll need two predictors that cover all the relevant variance and then do an F-test across both predictors to get the omnibus. Use whatever predictors best suit your need, as long as the cover all the variance (in my opinion, polynomials are best, as these will cover all the variance and be independent of one another). For example, you could have linear and quadratic predictors (i.e., linear = -1 for 1st level, 0 for 2nd, 1 for 3rd; quadratic = 1 for 1st & 3rd, -2 for 2nd level). Enter both these predictors, set the "Contrasts/F-Tests" drop-down to F-Test, enter 1 in the box, then in the row that appears below, enter 1 for both predictors. This will give you an F-Test across both predictors (i.e., the omnibus test).

For your second question, the toolbox cannot currently handle missing data. So, you either have to drop those participants or give them estimated values (e.g., via hotdeck imputation).