you could refer to the gas exchange methods as described here:
Measurement of substrate oxidation during exercise by means of gas exchange measurements. (2005). Measurement of substrate oxidation during exercise by means of gas exchange measurements, 26 Suppl 1, S28–37. doi:10.1055/s-2004-830512
But anyway, be careful - all of these methods (also the 13C-isotope method mentioned by Maxim) are influenced by the bicarbonate turnover induced from metabolic H+. This means that gas exchange is working (in theory) only at exercise intensities far below the lactate threshold. Of course, the challenge is to determine, where lactate threshold is located during discontiuous or long duration types of exercise ...
Best regards,
Kai
Article Measurement of Substrate Oxidation During Exercise by Means ...
Through spirometry you can calculate the Respiratory Coefficient and know efficiently what kind of substrate is prioritary being oxidized. Send you attached two articles that may help you.