If both disks have same size you can use dd command for cloning the first disk
Code:
dd if=/dev/sda of=/dev/sdb
If the second one is bigger you can do the same exercise and you'll have some space left on the disk which later you can partition.
If the first one is bigger but you think that the data can fit on the second, you can use gparted and to resize partitions on the first disk in the manner to fit on the second and to use dd for each partition
Code:
dd if=/dev/sda1 of=/dev/sdb1
dd if=/dev/sda2 of=/dev/sdb2
dd if=/dev/sda3 of=/dev/sdb3
dd if=/dev/sda4 of=/dev/sdb4
And if we are talking about linux system which you want to start from the second disk you'll have to clone the MBR with
Code:
dd if=/dev/sda of=/dev/sdb bs=512 count=1
This is for the third case, in first two the MBR is included