yeah, if you can, you want to be able to get some storage of the CLA. The only real way to do that is to take it with a meal that will raise insulin levels.
On low carb diets it really doesn't matter when you take it. I personally just take it at each meal (carbs or not). I take 5-6 grams per day, 1 gram at a time with each meal.
Now on the weekends when I eat carbs (i.e. bing), I really try to concentrate my CLA intake with those meals.
Both fish oil and CLA should be used this way if you want the effects they offer on fat cells.
Another thing that may or may not be important is the form you are taking. You can get both CLA and fish oil as free fatty acids or triglycerides. I have a hunch (I could be wrong) that the triglyceride form may have a better chance of making it into fat cells than the free fatty acids. Once in fat cells, as the cell breaks them down the fatty acids interact with intracellular PPAR-alpha receptors (& gamma to some extent) and do their "magic". The magic is that they reduce the amount of new fat the cell takes in and increases the amount of fat that is released from the cell when triggered to release fat.
The effect seen in research animals of raising metabolic rate are only acheived with large amounts of CLA. In general, you need to take 7 times more CLA than is given to mice in order to achieve a similar effect on BMR.