You may use either of the two. But if you charge only 2%, you will have to pay NBT more than you recover from the customer. For instance check following example invoice:
Rs.
Selling price 100.00
NBT 2% 2.00
...........
Sub total 102.00
VAT 11%* 11.22
............
Total 113.22
............
NBT Payable to IRD: 102 x 2% = 2.04
Here you have to pay Rs.2.04 as NBT to IRD although you recover only Rs.2.00 from the customer. Therefore you are not fully recovering NBT from the customer.
If you want to charge the customer the full NBT which you need to pay to IRD, you need to charge 2/98 (including tax on tax impact) from the selling price as NBT. Look at the following example invoice:
Rs.
Selling price 100.00
NBT 2/98 2.04
...........
Sub total 102.04
VAT 11% 11.22
............
Total 113.26
............
NBT Payable to IRD: 102.04 x 2% = 2.04
Here you can see that what you pay to IRD as NBT (Rs.2.04) is the same as what you charge the customer (Rs.2.04).
Can your customer refuse to pay NBT (either at 2% or 2/98)?
Yes. NBT is not a tax like VAT which you are bound to charge the customer and remit to IRD. Therefore customer can refuse to accept NBT unless otherwise agreed. So whether you can charge NBT or not will depend on the bargaining power of the two parties.