The feature has to be activated before it can be used. To activate it go in your merchant panel to  Start -> Plugins
Click the Activate or Buy button next to the Rest commissions.

The use of Rest Commissions enables the dynamic flow of commission tiers to flow uphill and can be defined per campaign. For example, you would like to pay out a total commission of 15% on a sale by paying the referring affiliate (1st Tier) a 5% commission, paying the parent 5% (2nd Tier), and pay the final 5% to the grandparent (3rd Tier or Top Tier).  However, if the referring affiliate (1st Tier) only has a parent and no grandparent, there would only be 10% to payout.  By using Rest Commissions, the “rest” of the commission gets paid to the affiliate that actually referred the sale.  So the 1st Tier Referring Affiliate would get 10% and the Parent 2nd Tier would now be the top tier and only get 5%.  If there is no parent, then the referring affiliate would get the full 15% commission.

If the main commission structure should be set to 5% for referring affiliate (1st Tier), 4% to the 2nd Tier, and 3% to the top tier (3rd Tier) the formula would be %3-%4-%5.  If you want to pay a flat commission instead of a percentage, remove the % sign so the formula would look like 3-4-5.  This structure defines tiers from right to left, where the tier on the right is the 1st tier, or referring affiliate.  Any tier missing to the left will get added to the tier at the right of the formula.  The affiliate on the left is the Top Level Affiliate (Highest Tier Number or oldest affiliate), with each tier to the right being one generation newer (i.e. it goes Grandparent-Parent-Child).

Example: in the case of five levels %2-%2-%2-%4-%5 the commission structure changes like this, if the last affiliate is missing:

All 5 tiers: %2-%2-%2-%4-%5
4 tiers: %2-%2-%2-%9
3 tiers: %2-%2-%11
2 tiers: %2-%13
1 tier: %15

Plugin configuration allows you to enable option: “Enable setting per commission groups”. If this is checked, you can set different 'Rest commission formula' per commission groups.