The guide for the product options is not yet available, it is still in the works. I think that there is a bit going on in this post and it will be difficult to address all of these things in a single response. I think it would be best to concentrate on one part of this, like adding the items with multiple options into the cart first.
Once we get that down we can look into the design or other add to cart scenarios. So rite now you have items that can have two type of options. In your example you mentioned an item that had size and color. So the first thing to do is determine how you would like to make the options available. If all of the items have the same options available this would be easiest. If only certain options go with certain items then you may need an additional table or tables in your db to hold the relationship between the options and products.
Either way you go the key to having the items add to the cart correctly is creating the recordsets for all of the info you would need. For example, if you have a simple scenario where the user can select the size and color of an option you could have recordsets on the page for just the sizes and colors. You could then bind the recordsets to select lists to have the user select the options they would like. Then when you add the item to the cart you would use bindings from these select lists or you would filter recordsets on the selected values to get back more details like the price for the option.
So the next question is how are the prices for the items determined, do the options figure into the price? If so are you storing the price or additional cost of an option currently in your options tables? You will need to make this determination and have this part worked out before you will be able to start crafting your add to cart pages. Please post back with the details for how you would like this to work from the perspective of the user and how the prices are figured. I will use your info to help you come up with a strategy to implement this.