I installed KonKart and can see the store with products and others things pulled from the pre-existing store.
I want to know if i run my local Konakart store , how can i define my own products and use it pull products into ,my liferay portal setup?
You can simply install KonaKart, define your products, run the ANT task to create your portlets for Liferay, install those portlets in Liferay and you're done!... follow the documentation for running the ANT task for creating the portlets.
There are some products which are per populated, how can i get rid of them ?
Look at the KonaKart Administration Application - you use that to administer your store.