If you don't want certain modifier groups or modifiers in a modifier group to show for your online ordering, you can simply hide them in YourMenu so they do not display!
To hide/un-hide entire Modifier Groups:
On the YourMenu dashboard, go to Menu > Modifier Groups and locate the group you wish to edit
Click the Edit button next to the Modifier Group
On the top of the edit screen, change the Availability to the correct choice
Not Available = Won't show on POS or online
Online Only = Will show online, won't show on POS
POS Only = Will show on POS, won't show online
Both = Will show on POS and online
Click Save
To hide/un-hide individual Modifiers in a group:
On the YourMenu dashboard, go to Menu > Modifier Groups and locate the group you wish to edit
In the Modifier Group, locate the individual Modifier you wish to edit under Modifiers
Click the Modifier you wish to edit and options will appear for it
On the right hand side, change the Hide toggle to on or off
Click Save Modifier
Click Save, to save the Modifier Group
To hide/unhide multiple Modifier Groups at once, you can click Quick Edit on top right of the screen. Once done, click Save!