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.

They CAN mean the same thing i.e that you saw someone had something in the past that they still have. BUT, I saw you had it can also mean that the person had something and no longer does.