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Anyone know if the NetSuite Commissions Module can handle different commission rates for different customers for the same employee?

i think so. you build a commissionable sales order search. apply commission plan/schedule on it.  you can go as creative as you want on that search.

Overall - feedback on NS Commissions is that you need to look at what it can do and then build your commission plan to match. Otherwise, I'd generally pass on it

There's normally some kind of wrinkle that doesn't fit with it that you either have to code on top of it with ASA or get overly complicated in the configuration

<@U05AC92BJE6> I only see a saved search function on commissions to handle eligible items, not customers or anything else. Am I missing something?

Can you provide more detail to your situation?  We use a custom entity field that holds our commission rates, then use a summary saved search and a CASE formula to calculate the commission owed.  There are a few other criteria, filters and a transaction updating workflow to consider but it's been a pretty workable custom approach to commissions for us.