My question is, are these two compatible? Is it okay to use both of them at the same time? Reason I ask is neither one of them seem to catch all of the conversions. Sometimes, one gets a conversion, the other shows nothing, or it flip flops, or neither one of them show a conversion when there was a sell. Of course, neither one of them will record a transaction when Google Checkout is the method of checkout.
You may be wondering why use both, it is a lot easier to see conversions in Adwords in the adwords manager or the desktop application for Adwords than it is to always have to go into Google Analytics and find the conversion.