It's a matter of deciding which you want to prioritize. If you're doing 5's progression or not really gunning for PR's, feeling crappy on a squat day from a long run/ride the previous day isn't that big of a deal if you get the work in alright. If you're really gunning for a PR, put the endurance stuff after the lift day, if you're ok with possibly feeling a little drained on it. For the cyclist, I do have to say if you're actually racing you should ditch the lifting other than the off-season (even then very debatable), but that's a whole other discussion. For templates, either look for ones that have long stretches between lower body work-outs that would give more space to get runs/rides in (like 2 day stuff, or the original 5/3/1 3 times a week or something), or experiment with more full body oriented stuff where low body frequency is higher but the volume is lower (Running or riding well the day after a 5/3/1 squat day would be more feasible than after a hard 5/3/1+BBB squat day). As with anything, as Jim mentioned, you still have to look at the overall workload you're taking on, some things may have to go or be reduced.
Really cool to hear this will be addressed in the new book, looking forward to the ideas on it.
Edit: If you're just running 3 miles though, that shouldn't be too much of an issue anytime, sorry I was more thinking about longer rides and runs above. I throw 2-3 miles in (running not jogging/shuffling) and it's not too much of an issue.