Personally, I'd make a backup of the E and F folder and FTP them manually to the new HDD.
Anyway, the XBox has the following partitions:
C - Dash storage, 349.95 MB
E - save games/DLC/songs storage, 4881.63 MB
F - only accessible in hacked dashes (max size of 939 GB iirc, without cluster size adjustment, 127GB)
G - only accessible in hacked dashes (same as the F)
X - swap partition, 749.89 MB
Y - same as X
Z - swap partition, 749.94 MB
If your dash displays those correctly then your partitions are properly created.
I've never heard of Chimp messing up tho, so I'm pretty sure you're good.
Just keep the old HDD as a backup for the time being until you're 100% certain all your data is copied over ;]