Should be fine: you put five gallons in a ~6 gallon carboy so the two 3's would be more less equal. I hear Fermcap can control foaming in the fermenter as well as the boil so that might help with high krausen levels.
Never split a batch myself though.
Enter the Labrewtory.
In Progress: Winter Siege ESB (Oak+Brett C)
On Tap: Homewrecker Bitter, Akron Fog (steam beer), Huckel's Yule (Xmas IRA), Winter Siege ESB
Planning: Deception Coffee Stout