Joomla 3.4, VM 3.0.6.2
I sympathize. I spend at least 10 hours of net searching before I got it right. I will try to summarize what I learned from all that searching. You may be well beyond this detail, but maybe it will help some other struggling person.
Add a custom field that is type multi-variant. I named mine the 2 variants I wanted like "size - color" because this title shows up above the input fields. You will only have one multi-variant custom-field in a product. It is kind of a "mega" field with the variant fields defined within it - called ramifications.
1. Add an new product and in Info tab put in product name, sku & price (take them out later if you don't want them but handy to test with)
2. Go to custom field tab. Add the custom field that you created for multi-variant.
3. A big box will open up. At the first dropdown, where it says product name, drop down and choose custom label. In the text area next to it, enter the label, e.g. size. (I found somewhere that if you are using built in attributes such as weight, you pick that label from the dropdown box - I haven't tried it.)
4. Enter the choices for the variant, one per line in the larger textbox to the right of the label text box. So if you are doing sizes, enter the S,M,L,XL one per line.
5. SAVE - This seems to be important at this step and sets things up to add the next variant.
6. A bit lower on the screen you should see "New Ramification." Click the little green round button just left of the text "New." Don't try to enter anything into the dropdown or the text box for the custom label until you have clicked the green button and it comes back with empty text boxes for the custom label and the choices for the variant.
7. Now you should have a new dropdown with product name (select custom label,) a text box for the custom label and a large textbox for the variants, say the colors. So you repeat steps 3-4 for the next variant.
8. SAVE
At this point you should have 2 variants, along with their choices, and a "New Ramification" box. Under the New Ramification should be a Add a Child Product button. If you had other variants, you could add them now by clicking the "New" button under the New Ramification. You could also add them later.
9. Add the child products. Click the Add a Child Product button as many times as you have child products. Or just start with 2 to test. You can add more later. The first time you click it, it will add a line for the parent and one child. Then each additional time for another child.
10. You should see a line for each child product that has a place for info like sku, price and also a drop down for each variant you added. The drop down will have the choices you entered in step 4.
11. Fill in the SKU & price if you want and select the variant combinations for each child.
12. SAVE. Note - when you go back to the product list, the child products will show "no price set." This is a small bug, if you open the child you will see the price carried over from the entries you just did.
This worked for me. I erred on my first try and added the multi-variant custom field for each variant - that was wrong. I needed to add a "new ramification" for the other variants after the first. And I found I needed to add the multi-variant custom fields and at least one child before doing anything else like adding other custom fields like string fields.
Hope this helps, but if you are already creating your product like this, then sorry, I can't help. Good Luck.