Fought squirrels non stop for last 4 years since I moved in this house to the point im going to start trapping them and shooting them in the cage. Yes the do eat tomatoes mostly when green they will take a bite or two and leave them laying. year before last had several huge plants The got pretty much every on before it ripened.Here's a pic of how I did mine. 6"x6"x8' treated timbers. 2 high. Drilled 3/8" holes and drove down 2' rebar to help keep together(probably should've used 3' and maybe 1/2"). Still have some warping after 4 years. I have the bailing wire up to keep the dog out(and to trip my wife...shhhh). You could put some chicken wire along the bottom and be able to step over. BUT, I think chickens can get a couple feet off the ground so not exactly bird proof.
I wouldn't worry too much about the squirrels but then again we have a dog. Never known squirrels to eat tomatoes or okra.
Yes, I'd get the manure/dirt into your beds this winter. As for ratio of mixing, guess that depends on how "hot" your feedlot dirt is(how much manure vs dirt). Will let someone else give input there. I used rich mix from a place in packing town then add a little booster each year.
Gardens are fun and much like anything else you get back what you put into it.