According to the champ web sight all gold members will receive a monthly stipend of 400 Cryptic Points to further enhance their game play. Now the cryptic points system is linked between the two games. If this continues can we spend the alloted 400 on STO instead or dose it have to be used on champ?

I not 100% sure, but I think you can spend them on STO, if you want. I received 400 CP when I bought Champions last year, and I didn't spend them until the C-Store for STO opened. I was allowed to use those points on STO C-Store items, so I would guess that you can use the CP you get from Champions in the STO C-Store.

We won't know until it's either announced or put in when it goes live. I would assume that they would keep things the way they are now, namely that CP can be shared between games. However, they might change it so that you can only spend them on the specific game that you buy/earn points for.

Turbine's points don't work for both LotRO and DDO. Each game has its own points. I wouldn't be surprised to see Cryptic go the same route.