Question about multiple CWDT setups

If I run 2 cwdt setups, will they share the 0.25s cooldown or will they be separate?

The cooldown is applied to the spell getting cast, not to CwDT itself. All copies of the gem will share the cooldown, but multiple CwDTs function entirely separately.

Example (a real one from a build of mine!): you have the following links.

CwDT (level 1) - Ice Spear - GMP

CwDT (level 20) - Discharge - Life Leech - Increased Critical Damage

Discharge - Life Leech - Increased Critical Damage - Lightning Penetration

You take enough damage to trigger the level 1 CwDT, and it casts Ice Spear. Ice Spear goes on a 250 ms cooldown. 100 ms later, you take enough damage to trigger the level 20 CwDT. It goes off and casts Discharge, putting all copies of Discharge on a 250 ms cooldown. For the next quarter second, the manually cast Discharge cannot be cast.

(Note that this applies to multiple copies of the same gem in a CwDT setup too. If you have two Ice Spears, say, linked to the same CwDT, the first will cast and put both on cooldown immediately, so the second one won't ever cast.)

I am currently using a high level cwdt with ec and ic, and just started using a low level one with enfeeble. Was just curious if both cwdt gems can proc at the same time, it's not like the 250ms cd is a gamebreaker.