Is there a compatibility patch for both mods for the updated versions if not what do you recommend.

No, the CPs haven't been made yet.

If you want to get the latest FOOK2 and FWE to work together, you're going to have to do some tinkering...
You'll need FO3Edit. And a pot of coffee.

See http://www.gamesas.com/index.php?/topic/1095717-facepalm/ for my account of the process.

So I have to tinker with FO3edit what do I have to tinker? Where di you get the FWE FOOK support?

Got a pot of coffee brewing? Okay... here goes.

First, get rid of all the FWE CPs.
I'm using the FOOK2 CPs for MMM and WMK, that's all.

Then, load up FO3Edit and build your merged patch. You'll probably get about a dozen or so errors.
Once the merged patch is made, you'll want to remove some records.

Remove the Creatures, Non-Player Character, Leveled Creatures, Leveled Items, and Leveled NPC records.
My merged patch contains only Containers, Factions, FormID Lists, and Race records. You may see something different...

Now do a "Clean Masters" on your merged patch, then do a "Check For Errors" on it.
Look at your Messages tab and see if anything pops up.

If not, exit FO3Edit and save the merged patch, then make sure it is loaded last in FOMM, then launch the game...

If it works, you win!!! If not, well... load up your mods in FO3Edit again.

You will have to go one-by-one through the individual records of your merged patch, and fix any of them that have invalid entries.

Save, check your load order, and launch FO3.
Keep doing this until you get Fallout3 to launch.
It took me about 3 or 4 hours to get it working...

But then, I was winging it too.

Oh... and running FOOK2 and FWE together like this... don't expect to get easy support from the mod developers.
Unless you know exactly what is causing your issue, and can explain it clearly in detail, don't even post a bug report.
That is understandable, seeing as the two overhauls conflict the way they do, if you forcefully squish them together this way, you are pretty much laying your own tracks.
These two mod teams have enough on their hands without trying to help people do things they tell us not to do.

Thanks.