Hi jindalarpan,
It seems to me that you want to make two identical machines.
I think the first thing you should take a look at is the active partition and/or the boot loader (assuming that the entire installation consists of /boot and /).
Using dd should wor if the target drive has the same- or bigger size:
Code:
dd if=/dev/sda of=/dev/sdb
If the original disk is /dev/sdb than you need to reverse the input and output parameters.
There is however a great interactive backup-tool called mondoarchive. This tool makes system backups even while the systems is still running. Take a look at
http://www.mondorescue.org/. If you're using the same hardware on both servers than this might be an easy way ;-).
This sadly won't help you with your partitioning problem.
Hope this helps.