Logistic regression eye treacting data (need model)

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I have two sets of time course data, they are for an eye-tracking study. The data is 20 100ms chunks, one category being percent fixations for canonical sentences, and the other being percent looks for non-canonical sentences. I would like to perform a fit on this which fits the data and shows how canonical and non-canonical sentences differ (or are similar). I thought placing the two averages under one another in spss and creating two new columns; specifically canonical and non-canonical. Next to the corresponding average for the time interval I would put a 1 in the canonical column and a 0 in the non-canonical column (and vise-versa). However, I'm not sure how to exactly set it up correctly because then I'm introducing two values (canonical and non-canonical) for one time interval and so I really need help. A nice model or some advise would help me out so much - I've spent days and days trying to read how to do this. Cheers!