You could do this a couple ways. You could either have separate campaigns setup to catch the form fill out with the different checkbox values:
Campaign 1:
Trigger - Fills Out Form
Filter - Checkbox Value is "True"
Flow Step 1
Campaign 2:
Trigger - Fills Out Form
Filter - Checkbox Value is "False"
Flow Step 2
Or, you could do it in the same campaign with if-then statements in your flow step:
Campaign 1:
Trigger - Fills Out Form
Flow - If Checkbox Value is "False", then flow step 1, If Checkbox Value is "True", then flow step 2