Migartion and partitioned disk

Hi all!
I am just about to migrate from my old MacBook to a new one. The old one has its disk partitioned on two parts - one for the operating system and one as a storage.
I am wondering if I just run the migration assistant it will do the same with the new HDD or it will only migrate the OS and later I will have to manually partition the HDD again and move the files?
Please, give any suggestions on how to do it with less troubles.
Thanks!

What I will do is that I will get a new MB and after I run it for the first time I will be asked if I want to migrate. I will say yes and will connect my old MB to it using USB (?) or Fifewire (not sure which one of those will be needed) cable.
Then I'd leave the computers to do whatever needed. This is how I already migrated one and all seemed just OK, besides that I had to insert some serial numbers again...
O believe I'll have to do the same this time, no? The only tricky part is what to do with the partition where I store my working files. You said earlier I need not to create any partitions, yes? I am used to those partitions since I was working actively on my PC, but if I somehow get convinced that the OS is secure enough, I may reconsider partitioning the disk.
So, back to the point:
1. How to make the computer ask me if I want to migrate for the second time?
2. After I run the migration assistant on first run of my new MB, I will migrate only the partition with the OS, no? Or I may chose (as I believe I see on the images you so kindly provided) other partitions as well? If yes, my question is if the migration assistant WILL or WILL NOT create the second partition for me?..
Thanks for getting involved with this! Thanks though!

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