Installment plan with efile extension

You cannot apply for an installment plan with an extension.  You can apply for an installment plan when you file the actual tax return.  The IRS won't approve an installment plan if your return is on extension and not actually filed.

during file an extension i put USD 9000 tax due I owe and then pay half amount now and later when file return in October i pay remaining amount. Is that amount subject to interest and penality? pls advise

Any balance due when you actually file your return will be subject to interest and penalty.  The interest and penalty is based on your actual tax liability, not the estimate you use on your extension.

that mean my total actual tax liability is 9000 and in file to extension i pay 4500 so the interest and penalty will be based on remaining 4500 m correct?

Not necessarily.  If when you file your return and your balance due is $4,500, then yes.  But if when you actually file your return your balance due turns out to be different, the interest and penalties will be based on that amount.