Putting aftermarket speakers with a stock headunit will def sound better if the stock ones are blown. No harm can be done by putting in speakers that are better. Just make sure that if you plan NOT to amp them, that they have a lower power rating or you wont get the full potential out of them.
It is usually wise to upgrade the headunit also as they will put out power watts.
Be more specific on what exactly you wanna do and use here would be glad to help!