Your 11Rack presets are numbered consecutively, so when you choose Bank 1, Preset 3 your 11Rack will be on Preset 03. When you change to Bank 2, Preset 1 your 11Rack will be on Preset 05; when you change to Bank 3, Preset 2 your 11Rack will be on Preset 10, etc.
I believe I understand what you want to accomplish, that being maintaining the same four basic guitar tones (Clean, Crunch, Rip, Shred), but when you change banks you want different effects parameters. For example, let's say for Preset 01 you want it to be a Clean tone with a very light chorus (Button 6) and subtle delay (Button 7), but while Preset 05 would still be a Clean tone, you want this one to have a heavy flanger (Button 6) and longer delay (Button 7).
If that's what you're after, in order to accomplish that, you should start by applying the bulk MIDI dump as described in the second thread from the top, titled...
Ground Control Pro + Eleven Rack Expansion Pack
Last time I checked it was directly above this thread. Following the instructions outlined there will get your GCPro and 11Rack communicating properly and your GCPro will be configured like this:
Instant Access buttons:
Button 1 = Wah On/Off
Button 2 = FX1 On/Off
Button 3 = FX2 On/Off
Button 4 = Tap Tempo
Button 5 = Distotion On/Off
Button 6 = Modulation On/Off
Button 7 = Delay On/Off
Button 8 = Reverb On/Off
Expression Pedal 1 = Volume Pedal in Eleven Rack Rigs.
Expression Pedal 2 = Wah position..
The next thing you should do is create your four basic 11Rack presets to use as templates. Once you've dialed in 01 Clean, 02 Crunch, 03 Rip and 04 Shred to your liking, them copy them to presets 5, 6, 7 & 8, then 9, 10, 11 & 12, then 13, 14, 15 & 16, etc.
Now you can pretty much forget about the GCPro for a while and start adding effects to your 11Rack presets. Once you've got the effects dialed in the way you want them, save that Preset on the 11Rack and move on to the next Preset. Keep doing that until you've created as many presets with various effects combinations that you need/want.
Now back to the GCPro. In Edit mode, starting with Bank 1/Preset 01, make sure the IA buttons are on for all the effects you want active when you first call up that particular Preset, and then save that preset on the GCPro. Repeat this process for each Preset.
This should get you there...
I can't read the manual for you, but odds are that's where I found the answer to your question.