Replace two old hard disk´s into one new on multi boot computer.

I have a Windows 7, sp1, computer with three disks one SSD and two old 500gb hard disks, I plan to replace the hard disks with one 1tb disk.

The SSD disk holds my Win 7 OS, disk no 2 do have all my programs, disk no 3 has one Win7 OS used for testing along with other data so this is a dual boot system. Disks 2 and 3 do have two partition each. While copying my disks I will have to move one of them out of the slot and but the new big one in permanently and then switch with the other to copy him, I have slots for tree disks.

I am going to use the test version of SSR 2013 for this project and plan to use the Copy My Hard Drive tool. I will have to do this twice because of the two hard disks copied into one new big one. My concern is:

1, I will put the new disk permanently into place and obviously switch the other from the former position, do this corrupt my programs drive letters.

2. Will the dual boot process be damaged.

3. Which should have been the first question, is this the correct process or is there a better one (e.g. use another tool in SSR)

Thanks in advance.