If you have a natural appetite for food, nutrition shouldn't be a problem. Smolov will cause you to stay hungry pretty much the whole time you're doing it, so if you like to eat, enjoy it.
If you don't have a good appetite for food, just discipline yourself to eat 4 whole food meals per day.
I wouldn't deadlift or do any additional lower body stuff during the base meso cycle or the intense cycle. As far as upper body lifts, just do your normal thing. If you're too wasted after your squats, which you probably will be, just do your main lift and an antagonist (for example, Bench Press with Rows) and be done with it.
Just keep in mind, it is a squat specialization program and you will not keep 100% of the progress you make after you go back to normal training. Plan ahead for that and don't be frustrated when those heavy weights don't move so fast or you can't even lift your new PR a few weeks after Smolov.
Smolov can be a great learning experience if you enjoy working hard in the gym. I think it is a great way to learn how to work REALLY hard in the gym. Smolov does make you a better squatter, not doubt, and you get a lot of practice with the lift in a short amount of time and it helps develop a bigger work capacity. However, I would agree, it isn't the best thing to use if you're looking to move your numbers up over the long term-- simply because you will still have to train to get back to that same PR over the next year or however long it takes you under normal training conditions.