You really should've read either the XDA thread or the CM Wiki before doing any of this...
Migrate to the one big partition for CM-13.0 :
- (Optional) Backup all your data, applications, internal storage, ...
- (Optional) Empty the internal storage with the old ROM or TWRP 3.0
- (Optional) If wished, do a full Nandroid backup from Recovery
- Flash the latest ROM zip of your device to start the unification
- Read and follow the instructions from the zip if anything goes wrong
- (Optional) Restore your Nandroid backup if you want to
- Flash the same ROM zip for CyanogenMod 13.0
So in other words, simply flashing the zip twice back-to-back will do.
Also, ditch CM recovery - it's not required and pathetically weak in function against TWRP. That will also allow you to connect to PC with MTP and put the zip inside the storage before flashing, which saves time if anything goes wrong (you don't need to
adb push again).