What happens when we want to format a computer and partition it into two drives then allocate the second drive to be the primary drive?

Delete the partition, then specify the different capacities of the drives.
'C' was the primary drive.
select drive 'D' as the primary drive and install the OS.
after installing, the computer will recognise drive 'D' as the system drive.

When installing Windows7 as an option and choosing the second drive, automatically the first HDD called "activate" and make100MB hide partition there being the kernel files of System Operate

The second drive (Primary) will be the will assign the letter (C:) and it will be the system drive.

First start a New windows setup - the steps changes with the type of windows that you would like to setup.
for windows7, when the setup reatches the the partition you should use to setup the windows in it, choose delete patition, and delete all partitions, then choose create new partition, choose the size of the partition you need, now you created the first partition, and the remains size shold be the second partition but you have to create it and write it size too, now you have two partitions.
format any one of them that you want to setup the windows on it, and it`s gonna be the primary partition.
hope this answer help full.,