Step 1: Components -- UserPoints -- Rules -- Custom -- Published: Yes
First of all you have to publish the rule. See above
Step 2: Components -- UserPoints -- Users -- Select user -- button "Custom points" -- Give/remove custom points...
When you give or remove points there come two field "Points" and "Description". If you want to give points, just write the number of points, for example 10. If you want to remove points from the user then use negative value, for example -10. You can also write short reason these custom points in description field if you want to. Last but not least remember Save all this, just press the button Save in the top right corner.
For example
Points:10
Description: Very active role in Community
Save
Step 3: Components -- UserPoints (Control Panel) -- Latest activity
If you want to check immediately those points what you just give or remove, see above. There you should see those custom points.