A Bill of Supply is issued when GST is not applicable on a transaction or when GST is not to be recovered from the customers. It doesn't matters whether your customers are Registered under GST or not.
There are mainly 3 cases in which Bill of Supply is required to be issued:-
1) If Supplier is a Composition Taxpayers- A dealer opting for composition scheme has to deposit tax on their receipts themselves, they are not allowed to collect any tax from their buyers. The GST has to be paid out of pocket by the composition dealer. Thus a composition dealer has to raise a Bill of Supply instead of a Tax Invoice.
2) If there is an Export- This is because export supplies are zero-rated. Hence a taxpayer exporting goods CAN issue a Bill of Supply in place of a tax invoice. But it is advisable for Exporters to issue Tax Invoice instead of Bill of Supply mainly in case of Exports with payment of IGST. Or mention it in Bill of Supply that Supply is meant for Export under payment of IGST.
3) If there is a Supply of Exempted Goods- When a registered dealer supplies exempted goods or services they are required to issue a Bill of Supply.
Now coming to the second part of your query,
If you supply Taxable + Exempted goods, then in that case you need to issue Tax Invoice only and mention in the Invoice quoting the Section No. that "Above mentioned goods are exempted, and hence GST is not applicable on them."
Remember there is nothing like Invoice cum Bill of Supply in GST, It is either Tax Invoice or Bill of Supply. But if you supply Taxable Goods along with the Exempted Goods then you will need to issue Tax Invoice because there comes a taxable component in that supply.
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