Can I pay a higher affiliate commission on some products?

Yes. In Affiliate Program, open the Commission Rules tab. Choose a Rule type (product, affiliate or category), enter its ID and the Rate %, then click Save rate.

When rules overlap, a product rule wins first, then an affiliate rule, then a category rule. If none apply, the Default commission rate % from Settings is used.

On Settings you can also choose Exclude taxes from commission, set the Cookie window (days) for how long a click still counts, and turn on Auto-approve affiliates.