Sorry, it's hard to explain and I'm not 100% sure if it is what is causing your freezing problem. If you can load the save and scroll to team management, check to see if there is a string of numbers (eg, 11898389918) in place of a players name in the starting 11 window that appears to the right. If so, this bug is likely your culprit.
As I was attempting to explain, you can use custom formations. You just have to be careful about how you edit them. The problem occurs when you edit a custom formation
after it is assigned to a team as its
default formation in the team management menu. You can edit/create formations without causing any problems, provided the saved formation you're changing
is not currently assigned to a team in either your MM team management section or in your squad file.
To give you an example, when I want to edit the formation -- let's call it Custom 4-2-3-1 -- I use as the default for my MM team I do the following steps:
1. Load MM save
2. From MM menu, go into team management --> formation
3. Custom 4-2-3-1 is the assigned formation (indicated with green checkmark)
4. Switch assigned formation to "team default"
5. Scroll back to Custom 4-2-3-1, press X/square to edit
6. Edit as you please and save Custom 4-2-3-1
7. Re-assign Custom 4-2-3-1 to be the active formation
8. MOST IMPORTANTLY: Never edit Custom 4-2-3-1 from Main Menu --> Team Management --> Formation while it is assigned to your squad in your MM save.
Step #4 is a safety net I started doing to be extra cautious after corrupting a MM save in FIFA10. Step 8 is really the key to avoiding corruption. I think the best thing to do is to make a group of formations solely for use in you manager mode and
never edit them outside of MM.
I am also weary of editing a formation during a game, but since I rarely, if ever, do so I'm not sure the best way to go about it. Probably just create a new formation I suppose. I wish there was a way to make temporary formation edits during a match like you could in WE/PES. It would make things a lot easier...