Is it a waste of money to have 2 boost control systems or is it smart? Specifically these 2

http://www.alteredatmosphere.com/mm5/merchant.mvc?Screen=PROD&Store_Code=AAM&Product_Code=45003-XK001

http://www.alteredatmosphere.com/mm5/merchant.mvc?Screen=PROD&Store_Code=AAM&Product_Code=TXS-DTEC-BC-PRO

My car is currently installed with the APS extreme duty turbo kit which generates about 1000HP.

Pick one or the other, you don't need both.
Not only would it be a waste of money it would be overly complicated and unnecessary. Pick the one that best suits your needs and has the features that you desire.
Having two would be like having two drivers seats, they would both work but essentially, you only need one to operate the vehicle.

Which one do you personally think is better?

I don't have much experience with boost controllers to be honest.

Although i will say that the Dtech sound gimmicky with being able to use a gameboy to control the boost controller and having the gameboy be a requirement in the programming of the controller kinda sucks.
that site doesn't seem to list what all the hks can do. plus the hks seems expensive at $600, i'd keep shopping and comparing.

Go HKS! I have an HKS EVC & I love it. I bought it used on ebay for $180... no need to flush $ down the toilet & buy it from a retail store... unless you GOTTA have it like that. Turbo XS has some good shiz, but I prefer HKS.