How do I upgrade base model ship like scout?

Two ways: either just build a better ship design in the shipyard and then declare the old version "obsolete", or build a better design and then use the Upgrade option when the old ship is selected, which will give you the option of upgrading it to the new type (providing the hull sizes match).
You can use Upgrade from the shipyard on ships you design yourself & then tweak them any way you like--but you can not do this to the base models, which are set in stone. So the best idea concerning them is simply not to build any; replace them with your own ships and declare them obsolete right off (but be sure to hit No when it asks if you want to decommission your original transport).
I build new ship designs on the very first turn, as many people do, because you can get faster transports and scouts immediately by adding even hyperdrive or ion drives to the base models.

If you declaire an older ship obsolete are all ships automatically upgraded?

Or is there a way of upgrading all ships on one type to another type?

--Steve

I upgrade by singling out one of the older designs on the main map, selecting it then clicking the upgrade button on the ship details panel at the bottom of the screen. From there, you select the design to upgrade to, then check the "upgrade all ships" box and select your payment plan.

If you upgraded a currently existing (user) design, any starports building the older model will switch to the new design.

Cheers,
Reaver

I think the OP is asking how to upgrade the flagship or colony ship that you start the game with. As far as I know, there is no way to do this.

One wrinkle of this worth noting is that the anomalies that give a ship an experience bonus are utterly useless if you survey them with your flagship.