Lets start with the scenario:

The user clicks into the details page.  He can then choose whether he wants small, medium or large, then selects blue or black, then selects gold imprint or silver.

These options are not additional costs, they are just walking the customer through the process of selecting which item to buy.   Each item has a different price - ex. the large is $50, medium is $40 and small is $30. 
I only see the option in ProductCart to enter the additional price added onto the base price for the options.

Any help would be greatly appreciated.

Product Cart (as well as many other ecommerce packages) handle this scenario as one product with multiple options and the options can have additional pricing. In your scenario above, the base price could be $30. Then the options would have the following additional prices:
Small - no additional price
Medium +10
Large +20

If you need more control over the options, want to track inventory by option and/or want to have different pictures for the options, i.e. different colors, you should look into the Apparel Add-On. See details here: http://www.earlyimpact.com/productcart/apparel-software.asp - http://www.earlyimpact.com/productcart/apparel-software.asp

If you want each option to be an actual different product, you could use categories and subcategories although this is not usually as clear to the customer. For example, you could have a main category called Shirts then subcategories for the style of the shirt. Once they choose a style they could choose subcategory for Small, Medium or Large and then just have the color as an option.

This is not the ideal way to handle this but it can work.