Does the vote up and vote down in MSEmeta affect the reputation in MSE or the converse. Also why is there a difference between the reputation of MSEmeta and MSE. They are fairly close in my case, just wondering.
Voting on meta.math.SE does not affect reputation anywhere.
(However, the badges you gain on meta.math.SE are separate from your badges on math.SE.)
Your meta.math.SE reputation is a copy of your math.SE reputation, though sometimes it takes a few hours to update to the latest value. This is how all meta.____.SE sites work, except for meta.stackoverflow.
Meta has no impact on your main reputation. Instead, your meta rep is exactly your main rep, with any discrepancy caused only by a small latency between rep changes on main being updated to your meta account.