Use the HT bypass. That's what it's for and it works great.
I have a line 3 SE too & I use separate interconnects. I think there are a some considerations to take into account, tube wear & to a lesser extent additional electric usage. Also, do you want to use balanced interconnects? If so you can't use the HT bypass with balanced IC's. I also had a problem with a ground loop in my system when I used the HT bypass that was difficult to track down, I'm not saying you will run into the same problem but it could occur. The downfall - my wife can't watch a movie unless I already have the IC's hooked up (oh well). Just my two sense.