You could also consider the opposite approach, which is probably less intuitive for a musician, but it can achieve far more precise and controlled results.
Record everything at tempo with the metronome and then use the tempo track to make all the rubatos, rallentandos, accellerandos, breaths etc.
There are two definite advantages with this approach: first, everything syncs beautifully without any extra effort (with the other method, it might take you hours before you have everything in perfect sync) and second, you have absolute control of the tempo, which means you can change your tempo “waves” any way you want, allowing for more experimentation.