Perhaps I didn't understand you but if it is the way I understood then maybe this could help.
I had a similar problem and I solved it the following way.
The trick is that you write your data to Excel always in the same way, i.e you use columns 1,2 and 3 for your x values and column 4 for your Y values.
Then you write your own sub routine within the macro you recorded (I don't know if you are introduced to VB, but even if you dont it shouldn't be too hard), this way you'll know exactly where your data is and how much data you have.
After that you change the recorded values in the seriescollection to the ones you get from your own routine.
I hope this will help you.