first order of business for me if it's raining is to set up a tarp over picnic table/cooking area first.

this gives you a spot to park the bikes and dig around in your panniers without soaking them and get some hot tea water going under cover before you set up tent.

i usually just set up in the rain; setting up tents with seperate flies aren't that bad; like others have said, just be quick about it. If its really raining, with a tarp pitched you can partially set up tent under the tarp, then move it to where you are sleeping in it.

Additionally, a grizzled Northwesterner trick is to set up tent UNDERNEATH a big tarp..... makes very nice sleeping conditions and a mostly dry tent underneath.....