Goodness ... you don't have to open up a separate thread just ask for answers.
1st thing of all, the payment method are out outlined in your T&C pack (when you collect your card) + they are also mentioned in your statement. (Look at the back of your statement and sometime printed as well at the front) So, the excuse of not knowing you have to pay separately would not arise. Payment methods are different when it comes to Principal and Supplementary cards and again this varies from bank to bank.

Just call CS to help you. If can then they will help. So long you did pay the RM4K within the due date, there's hope. (If you paid late then your chances/bargaining power decreases) Please bear in mind that this does not alter the information for your credit history if the correction is made. And remember to ask nicely, don't force or barge your way for them to help you. You made a mistake in the first place. Apologize and ask nicely but don't force them. CS does not have the power nor juristristion to make the amendments. They just capture the info and pass it on to the other department. You can't ask to speak directly to that department - it doesn't work that way.

If not, just take it as an expensive lesson. Next time, take your time to read the T&C - don't get excited owning a credit card and when a mistake happens, you say you are ignorant whereas all the info have been given to you at the point of receiving the card. I do not want to sound so optimistic because banks will always treat cases like these on a case to case basis. What works for others may not work for you.

Your story sounds confused but yes, payment for MY CC's is nearly always based on per-card basis (I'm not aware of any which does not do this). Having the same credit limit makes zero difference in terms of payment.

Your first scenario can be termed a newbie mistake but asking if you should get charged interest if you didn't pay in full is a bit too much... 

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Added on March 16, 2011, 12:52 am

Makes no difference, you will not be able to speak to someone who can actually make a decision either way. Worst case scenario is just paying the late fees and interest.

Late payment for CC once or twice per year makes little difference to your credit record. In fact banks would prefer you frequently pay late (but not till the extent the bank needs to come after you for payment).