USD mostly.
Bitinstant charge like 3.99% for transferring. Isn't it is must more better to send thru btc addresses provided by bitstamp and btc-e itself? Or it is not advised to do so?
Kindly enlighten me please. :-)
It's very hard to get USD into BTC-e. It's much easier to use another cryptocurrency and send that into BTC-e. So buy your BTC on Bitstamp, and then send the BTC to BTC-e directly using your BTC-e Bitcoin address.
Bitinstant is only useful for transferring USD around from one exchange to another, but it's not always reliable and it's not always available, and it's expensive. So basically once you get USD into the system on some exchange, just buy BTC, and then transfer the BTC (or other cryptocurrency like LTC) around between exchanges.