[Rutherford]

The molecule is attached.
1.How can I determine the absolute configurations of the three chiral atoms in this molecule? I don't know which substituent is under or above the plane.
2.Why is the name of this compound 1-bromo-3,4-dimethyl-cyclohexane and not 1,2-dimethyl-4-bromo-cyclohexane?

EDIT: I made a mistake. Now it is attached.

[discodermolide]

Wherever the molecule is it is called 4-bromo-1,2-dimethylcyclohexane according to ChemDraw.

Make a model of this compound and you will see what is up and what is down.
In your drawing it is not clear if the methyl and bromine are axial or equatorial, you drew them as straight bonds. See drawing.

[Rutherford]

What do you mean by model?

[discodermolide]

Use balls and sticks to make a model of the compound . Then you will see what it looks like.

[Rutherford]

I didn't draw this and I don't have balls and sticks. I will try now, when they are equatorial by imagining.

[discodermolide]

OK let's see what configuration you get.

[Rutherford]

Wow, this is tough. Somehow I got all S.When I look from above at cyclohexane, are carbon 1/6 and 3/4 in the same plane?

[discodermolide]

That's correct, you got it.
See pic

[Rutherford]

Okay, this is solved then. Thanks.