You have two options:
1.In cases where you have made lower deductions, change entries in the books of account making deductions at the appropriate rates and remit the additional amount to the Government along with Interest aplicable.
2. The other option is to change entries in the books to deduct TDS at appropriate rates for both cases where you have made deduction at higher rates and at lower rates. After you do this, you may find that either you have remitted excess TDS to Government A/c or remitted a lesser amount to the Governement A/c. If you have paid a lesser amount, remit the same to te Governement A/c along with Interest.
This is as per my knowledge. But do wait for opinion from someone who has more indepth knowledge.