I've found that when creating the project plan, you initially discuss the amount of time that the resource can dedicate with their manager. With this information you adjust the plan with the % available and let the software determine the schedule dates using the % times the duration required. If this schedule isn't going to work, it will be apparent up front and allow time to either negotiate with the manager or escalate to the sponsor. If during the project the resource falls behind due to other work, you have commitments from their managers that you can use to regain resource time. The whole key is to have a commitment up front from the manager and to know how that commitment will affect the schedule.
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