I use a frameless pack, Jam2.
If it is raining, I will empty everything in the pack and place the pack under my legs, in the bivy.
The space above my head in my Mountain Laurel Designs Soul Side Zip Bivy is large enough to hold all of my gear and protect it from the rain.
Things like my MSR Kettle, platypus water bottle, and other things that I am not worried about if they get wet are outside my bivy, under the tarp with in arms reach from the bivy.
If I am not expecting rain, I just place my empty pack under my legs, under my bivy.
I carry a garbage bag as a pack liner and I will store my shoes in them and keep them in or outside the bivy, depending on how heavy the rain is.
Otherwise, in not rain situations, I will place my shoes under my bivy and position them to be my pillow.
Hope this helps.
Hope that helps