Is thier any way of setting Waypoints with the System? I see the option for adding Multiple Destinations but I only want one Destination. Multiple destinations messes up the Estimated Time of Arivial.

YES.
You set the 1st waypoint, and when you enter it, it will prompt for replace or add to destination. Use replace.
Then set the 2nd waypoint and when you get the prompt, choose add.
Then set the final destination and when you are prompted, choose add.
That is all there is to it.

As you surmise the total end to end time of arrival won't be available.

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Correct me if I'm wrong but I thought there was no actual way to set a waypoint. I thought you had to add a destination that could essentially work as a waypoint. So if you want to take a specific road to your final destination and one of the three routes offered by the Nav system doesn't use that road then you could add a destination on that road and it will guide you to that road and continue on...

I also don't think adding multiple destination will mess up the estimated time of arrival to your final destination. The estimated time is based on reaching that point and continuing on. It doesn't take into consideration if you are stopping or not. As you add destinations your estimated time of arrival should change based on the increase/decrease distance to your final destination.

What I usually do is set the final destination and choose the best of the three routes offered. Once I figure out which route is best for me at that point I will add additional destinations (essentially creating waypoints) to fine tune my route the way I want to go.

Actually the ETA to the final destination AND all the intermediated points is available.
The destination graphic/icon is "clickable". Just press and it expands to show the various destinations and their ETA or ETE which you can switch with the rightmost icon after you expand them.