You really could go either way, the line is there more to vent crank case gases and pressure more than vaccum them away. The only thing is you might need to change the breather on a regular basis (maybe like every two or three oil changes) since it will inevitably get clogged with oil. So it might be better to go with the hose as far as your wallet is concerned, or if you think it looks better with the breather filters then go that way. I say it's up to personal preferance. I put on a breather on the crankcase and opted to cut the connection point on my CAI tube. I put the IAT sensor in there at first, but after I got the larger injectors and the Apexi SAFC2, I relocated the IAT sensor to the stock position and intstalled the jet for my alcohol injection setup in it's place on the CAI tube.
1999 4.0 WJ Limited NX Wet EFI Kit;HESCO Head, Cam and Water Pump;Apexi SAFC2;Accel 24lb injectors;K&N FIPK; 2.5" Dynomax Ultraflow SS Exhaust; Dynatech Cat; Banks SS header;Custom 3" Head Pipe;E Cut-out;62mm TB & Spacer; MSD DIS-4; Jet 180°stat;H&R springs;Eibach Sway Bars;Brembo Rotors; Streetscene grill;E.L. Dash ; Autometer C2 EGT, N2O & Fuel Pressure;Edlebrock A:F Meter