use a master slave scenario to accomplish my project or 2 separate arduinos

I am working on an aquarium controller based on a mega 2560 r3 board with a wiznet 5100 ethernet shield.

I am thinking about using ws2812b light strips to create a sunrise/sunset moon rise / moon set lighting scheme with cloudy days and lightning storms mimic real life.

right now i have a lot of the pins on the mega occupied controlling pumps etc.
and what i have read so far about these lights is they don`t play well with millis in a sketch which so far my controller sketch has quite few.

should i just get another arduino and dedicate it to the light control separate from the tank control or should i be looking at a master/ slave scenario

also i will be controlling possibly 1200 leds on 36 separate strips so which arduino would you suggest i use for the lighting control

Having the Mega tell a Promini what to do sounds efficient to run the ws2812s.
Are the separate strips individually addressable, or "dumb" strips, segments of 3 LEDs in series powered from 12V? If so, I have a MOSFET driver board the promini could control to drive the LED strips. 32 channels, daisy chain two if you really need 36.
Here it is with a Duemilanove mounted on top with some standoffs.

the separate strips are addressable.

i am picking up my first 5 meter strip after work tomorrow the supplier i am getting them from also sells arduinos almost any model that is available at very reasonable prices mega 2560`s are $19 his lowest priced one is around $4 so which arduino do you think i should use ?

this is going to be an extreme undertaking since i am new to arduino but have learned a bunch in the last few months made a lot of progress with lots of help from people here and on other forums with lots of head scratching and cursing to myself how the @#$% can i make this work.

thanks for the suggestions

looked at your boards very nice!!!!!
i am thinking one of your mega screw shields will make my life a lot easier!!!
my wiznet 5100 ethernet shield should just stack on top of the screw shield correct?

Which board is up to you - addressable strips, which interface do they need? I think some types are easier to have multiple units of than others.

Yes, shields will stack on top of the screw shield.
Kits & assembled boards are available, $35 and $50 each. PM me with your address details, I can let you know USPS shipping costs.