You can enter a tax exempt ID on both your customers and leads. On the lead, when you choose that the lead is tax exempt, an input will show that allows you to enter the exemption ID. On the customer, the exempt ID field is shown always, except when viewing the customer from the lead. You must go directly to the customer record.
If you set a tax exempt ID on a customer that is on the lead you are working with, you will get a warning message asking if you also want to make the lead tax exempt. Choosing 'Yes' will make it exempt and copy in the customer's exempt ID to the lead.
Don't forget you can attach their tax exemption certificate to the customer and/or lead to make it easier to find it if needed. You can also filter on the exempt ID as well as include those fields in any report you build.
See the video below to see how it works.