I think some more detail is needed. What are you measuring?
Maybe some general guidance will help (I hope). First, each column of your data table needs to be a variable. Each row of the table is an observation. You want to compare the means of different groups of data, correct? If so, then you need a column that identifies the group to which that particular observation belongs. You need another column that identifies the item that you are measuring. For a t-test, that item would need to be a continuous variable.
From your description, it sounds like you want three different comparisons: A1 to B1, A2 to B2, and A3 to B3. That would result in six column in your JMP table, structured something like this:
Then you can choose Fit Y by X. The Group variable goes in as the X. The measurement variable goes in the Y.
If your data is not structured this way JMP provides lots of ways to manipulate it to this format. Look at the Split and Stack commands under the Table menu. You can also ask for help in the community if you need help getting it into the proper format.
Dan Obermiller