What you have to do is to connect the AudioIn to some modules into your patch. The simplest way to do this is to connect one of the AudioIn output (L or R) to the VCA1 (named OUT1 on the GUI).
Apply the following steps:
1- load an empty preset
2- open the OUT1 zoomed view (navigate to the OUT1 cell and click 1 time)
3- there navigate to the AUDIO popup under the text "INPUTS" on the right panel of the zoomed view
4- click on the popup button (which should display "NOT CONNECTED"), this opens the popup "window"
5- navigate to the "Add Connection" option (using the arrows switches or the large knob above the arrow switches), and click, this opens up a new popup
6- navigate to the "Inputs" entry, click, this opens a new popup window
7- navigate to "Audio L" or "Audio R" and click
8- go to HOME/SETTINGS/System 2 page and there enable the "Audio IN Auto Start" option
9- save your preset and reload it.
The "Audio IN Auto Start" option may look somehow mysterious and indeed it is
This option enables the sound of the "Audio L/R" input to actually be processed by the OUT1 module without the need to play a note on a keyboard. What it does is that it says to Origin to internally generates a fake note when the preset is loaded.
At this point, connect your guitar to the "Audio L/R" (whichever one you chose at step 7 above) you should now hear the raw sound of your guitar at the outputs of Origin.
Now you can select the effects on the "FX" section and choose there a reverb, a chorus or a rotary speaker or whatever you like. You can also edit the "PATCH" ("Edit" section). You could connect the "Audio L/R" signal to the a filter input (and the filter output to the VCA input), set this filter as a resonant band pass filter, and assign the expression pedal to the frequency of the filter. You've got there a wha wha effect. You can also connect one of the main LFO (LFO1 or LFO2 in the "Progr" section) to the AM input of the VCA. You have added a tremolo to your effect chain.
Have fun.