There is something funny with this, like manual won't show up if the camera is connected to the USB or similar, I don't have FoCal here so can't check, but it is not the easiest option to find.
I think this has been mentioned in a thread before if you know how to make the forum search provide you with any useful results! It never works for me.
Calibration Target Set Up
Analysis and Re-Calibration (if needed)
1. Remove the memory card, download the photos to your PC/Mac
2. Launch FoCal, select Tools>Manual Mode
3. Click on Add Files and select the shots you just took
4. When they appear, make sure the AFMA values appear correctly (they should) and that you took all of the shots required
Looked at this, but cannot see any Manual Mode option.
7DII+Grip, 7D+Grip, 40D+Grip, 5D+Grip, EF 24-105 f4L EF-S 17-85, EF-S 10-22, EF 70-200 f2.8 L IS II, EF 2x III, EF 100-400 f/4.5-5.6l IS II, Σ17-70 f2.8-4 C, EF 50mm f1.8, 550EX, Triopo TR-985, Filters Remotes Macro tubes Tripod heads etc!
5D, 20D, 24-105, BG-E4, BG-E2N, 17-85, Nifty 50 pre owned.