Currently I'm taking magnesium malate, calcium citrate, b6 & zinc picolinate alongside methionine/tmg to try to lower histamine levels.

I know that some of these conflict with each other. Obviously magnesium and calcium but I also read on here that b6 & zinc can fight for absorption and b6 could deplete magnesium in the body.

I do not like individual B vitamins.  They are best taken in a form where the B vitamins are combined such as yeast, rice or oat bran, seaweeds, etc.  Of even as a low level B complex such as a B50.  High doses of individual B vitamins can displace other B vitamins.

I would not worry about B6 interfering with zinc since you will not be taking enough of either to be an issue.  When things compete for receptors there are only so many receptors so one compound will win out over another if enough of something is taken to lock up all the receptors.  But in the small amounts you would be taking of B6 and zinc there would be no significant competition.

Can you give me advice what to take with what/what to separate. Also what to take on empty stomach/what to take with food.

What you mentioned should be taken with food, especially the zinc.  You want to do this with your larger meals.

As for calcium and magnesium this will depend in part on what you are trying to accomplish.  If building bone then these can be taken together in smaller frequent doses.  If using magnesium though to relax muscles or lower blood pressure though the magnesium levels should exceed calcium and should be taken separately from the calcium.