It's kind of confusing. So first, that whole sentence can be split into two. Ex. "I would say the most difficult thing is that we have deadlines. I'll be given a project and..." The 'so' and the comma makes it that the two sentences can form one. That is why it is able to have two different topics and two different tenses. Hopefully that is helpful. I tried to describe that the best I could.

Well, "I saw you had it" and "I saw you have it" are the basically the same. "I saw you had it" is saying you saw the person had it before, as in pass tense. "I saw you have it" is saying you saw the person has it now, as in present tense. The way you would use "I saw you had it", would be you saw that the person had it and went to talk to them later. The way you would use "I saw you have it" would be if you saw that person having it and went to go talk to them immediately. Both of them are correct. Hopefully that helps. As for "What do you understand this?" and "We don't go through it", both need some changes. "What do you understand this?" could be changed to "What? Do you understand this?" or "What, do you understand this?" (mainly the first one). "We don't go through it" is basically saying "We do not go through it". So "What do you understand this?" would be better if changed to "What? Do you understand this?" or something similar. "We don't go through it" (We do not go through it) can be used.