Well, you have to do a lot of research, because not all shuttles are the same.
Many will have just a few drop off and pick up times, and they will only drop and pick up at one park (Epcot seems to be a popular one for this, and the TTC is another spot). So if you are going to a park other than the drop off park, you would have to allow extra time to get to that park and return from that park to the drop/pickup point using Disney transportation. You also need to be sure you are at the pickup spot before the pickup time, so you don't miss your bus.
Sometimes it's better to stay where there is a small fee for the shuttle, because those often have more trips scheduled, and some even allow you to call from the park to reserve your pick up time (they let you know when the next bus will be at your location and schedule you for it) so you can be more flexible about leaving the park. But if you have a large family, this can get expensive.
Either way, you may find that you can't get to the parks for rope drop or stay until closing when using off property shuttles. You need to check directly with the hotel you are considering and see what is involved before you book your room, so there aren't any unpleasant surprises.