I think there's two things to bear in mind here:
1) Where to put them in a routine
2) When to add them to a routine
In terms of where, they will never be the main exercises of any routine. When compiling a list of the most effective exercises for mass most types of free weight exercises will be superior. But I used to like isolation/machine exercises for those days when you still want to work a bodypart but are perhaps going to go light.
Example 1 - A chest portion of an intermediate bodybuilder routine:
Day 1: Bench Press 5 x 5
Day 2: Machine Press 5 x 15
Day 3: Incline Press 5 x 12
So in this case the machine/iso exercise is being used to split up the week and provide some light work between heavier sessions.
Example 2 - A chest routine of a more advanced natural bodybuilder.
Day 1: Bench Presses 5 x 5 , Incline DB Bench 5 x 10
Day 2: Pullovers 5 x 15, Machine Presses 5 x 15
Day 3: Incline Presses 5 x 12 , Machine Flyes 5 x 12
In this example machines/iso's are used to provide extra work however the core of the routine is/are still free weight exercises.
So we've considered where now if we discuss when a little. The when is really determined by your own needs, a beginner can still make good progress doing 3 basic exercises per bodypart spread across the week and that would be my recommendation. Once progress on that has been exhausted further work can be added and this should usually be in the form of isolation exercises which don't aggravate joints and/or tendons. Obviously there is a cap to this volume increase, you can't keep adding volume but that will depend on factors such as work capacity and goals.
Hope that answers your question.