If you don't have room to clamp the bottom template use double sided tape.

 

Most two sided jigs use a guidebushing and a smaller bit and make a pass up one side and down the other to get a perfect width.
In your case, a one sided guide/jig may lead to a "worbble" if you don't hold the router fast to the guide. DAMHIKT!
You are correct about warped boards on the table saw leaving inconsistant depths! DAMHIKT!

We need to know if your dados run lengthwise or across?
Take a photo of your setup, and we can offer better advice. I've been makin' dados for about 40 years, mostly with the table saw for cabinetry or Radial Arm saw for across the width on shelving.

 

So if I understand your problem the board you want to fit in the dado is cupped and does not fit the dado. You can't flatten the board enough to jam it in the dado? Have you tried clamping a caul to the cupped board to straighten it? Have you tried wetting the concave side of the board so it will expand and flatten?
Making a dado wider than it needs to be looks sloppy. I suggest you work at making the board fit. You could build a modified jig that will allow you to use your router to plow a dado that matches the curve of your board, but I have never met a cupped board that I couldn't jam into a dado. This must be some heck of a warped board.

 

So if I understand your problem the board you want to fit in the dado is cupped and does not fit the dado. You can't flatten the board enough to jam it in the dado? Have you tried clamping a caul to the cupped board to straighten it? Have you tried wetting the concave side of the board so it will expand and flatten?
Making a dado wider than it needs to be looks sloppy. I suggest you work at making the board fit. You could build a modified jig that will allow you to use your router to plow a dado that matches the curve of your board, but I have never met a cupped board that I couldn't jam into a dado. This must be some heck of a warped board.

I would concentrate on the board rather than the dado.Hand plane a slight angle "leadin" so it will "force feed" into the dado without excess play.
That way it's easy to adjust the fit.

 

If you can't straighten the cup enough to fit the dado, you could try cutting a slightly narrower dado, and then make rabbets in the cupped board, to create basically a fat tenon. The rabbets would remove the edges of the concave side of the cup, and the center of the convex side.

 

If I understand correctly, your issue is that the top and bottom dados are too close to the ends of your work piece and you lose support for one side of your template. If this is correct, just use some scrap of the same thickness to support the template. Secure it to the work bench with 2 sided tape or clamps or what other means you might have.

 

^^^this

If you think ahead you can even cut them next time before trimming the piece to length.

Cupped boards are a completely different problem.

 

The cupped board is not the problem because I am using a spacer from the original board so it gives a clearance for the cut. Using the table saw was giving a fit because the dado is close to the edge, my board would walk a little so I decided the router. I hope this will clear up some confusion. The pictures attached show my setup. Someone here suggested using double sided tape. I may try that to see if it holds with the pressure of the router running against the fence and slight down force from my hand. Yup, I think this is my next try. Wood is too expensive to keep making mistakes and limits practice cuts.

 

I'm still not sure what you are attempting to do? Sorry.
It appears that your router jig is several feet longer than your workpiece.
In addition, your work bench, a workmate, is not wide enough for supporting the jig. That will add to your difficulties.
Can I suggest two saw horses and a slab door as a temporary work table?
I would work with a short straight edge guide rather than a long jig.
You can use the router OR a circular saw to just slightly enlarge the width of the dado for your perfect fit, assuming that is your issue?
OR if it were me, I'd go back to the table saw with a single blade set at the correct height and a featherboard on the fence to keep some down pressure on your warped board. Realize that will only effect the depth, not the width of the dado, unless you need to make it wider than at present, in which case you would adjust the fence.
We are talking about a a 1/64th of an inch or less, what ever it takes to fit the pice into the dado.
I suggested abpve work with ahandplane to slightly taper the end of the workpiece for the most accurate fit possible, shaving off only a few passes at a time.
You are "fine tuning" the fit of your existing dado, IF I am understanding this whole issue?