Quick question when building a team, say it is 300 pts.
do you use the point values of the starting figures or the ones the promote into?

When building your force, you use the point value of whatever character you're using. So if you're using Robin from the 10th Anniversary set, you play him at 52 points (his point value). If you happen to promote into Nightwing via his trait:

That's fine. However if your opponent were to KO Nightwing, they would get the 94 points he's worth (I believe). Unlike the Alter-Ego mechanic or the Morph mechanic, you're replacing your figure figure with a figure of a higher point value (usually) opposed to a figure of the same point value. Now at what point value that figure comes in at depends on what the battlefield promotion trait says for that character. But here it just says "replace with Nighwing on his same click number". So if your opponent KO'ed him, they would get 94 points since they did not KO Robin, they KO'ed Nightwing and Nightwing is 94 points.

On the flash where it says, Flash could use Charge and flurry, when he uses charage he can also use exploit weakness.Does this mean I have to choose between charge and flurry and exploit weakness. Or can i use flurry and the damage is penatrating

You believe correctly.

You should make sure to quote powers...

No matter what, Flurry and EW are incompatible. So if you choose Exploit, it won't work with Flurry.

Correct.

Alternatively, If a Shield Disruptor object is within 4 squares of Flash and his target, damage dealt to his target will be penetrating (and vice-versa). Outwit is another option to counter a damage-reducer.