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For step 2, if you want to have enough withheld from your pay so that you do not have to pay in at the end of the year or that you get a refund you will look at the table on page 4 of the W4 to find your answer.  

Say you are making $101,000 and your wife is making $43,000.  On the right of the table under Married Filing Jointly you will look at the column that says $100,000-$149,000 then at the top you will look for the row that say $40,000-$49,000 and find the point they intersect which in this example is $8,370.

You will enter the $8,370 on line 1 of your W4 page 3, then you will divide this number by the number of times per year you get paid.  So if you get paid every other week, you would divide $8,370 by 26 for a total of $321.92.  You would then enter the $321.92 as the amount you wanted for extra withholdings on Step 4c of your W2.

The purpose of this is so that you are taxed at the rate you should be with both incomes taken into consideration instead of just your income counted.  

The fact that your wife is self-employed does not affect how you will enter this on your W4, especially since she is making quarterly payments which kind of act the same as if she was employed and an employer was withholding taxes for her.