Product is "T-shirt & Shorts"
Option Name: T-shirt Size Option Values S, M, L, XL
Option name: T-shirt Colour Option Values Red, Green Blue etc
Option Name: Shorts Size Option Values S, M, L, XL
Option name: Shorts Colour Option Values Red, Green Blue etc
I'd also recommend that each Option Name has an initial, pre-set value of "Select from below" (or "Please choose") to force your customers to tell you what they want - do that by setting that value to:
Used For Display Purposes Only: Yes
Default Attribute to be Marked Selected: Yes
If you want to charge extra for certain colours/sizes then you set the base product as Priced by Attributes and, in the Attributes Controller, put the price difference from the base price against that value.
I also strongly advise you to insert bunyip's recent Attributes Controller mod (Downloads section) - it's a single file that replaces the core file and will save you hours.