When your EMI bounces, you will have to pay a late payment fee. This fee differs from lender to lender and the charges might increase if the payments are not made immediately. On the long run, your credit score can get affected negatively. Missing out even one of your EMI payments will bring down your credit score. With your credit score down, availing new credit in the future will become difficult. There is also a possibility that lenders might follow up and ask you to make the payments. If you fail to make payments in spite of continuous reminders, legal action might be taken against you.
So if the cheque you had paid for EMI bounces, you would have to pay a cheque bounce charge along with late repayment fees. To pay your EMIs regularly, you can start managing your spends accordingly. Making regular EMI payments is better than making late payments and pay additional charges for it.
Additional Reading: 4 Things to do When You Cannot Pay Your EMIs