Trying to container garden on my back porch

Trying to container garden on my back porch

I'm in my second season of trying to container garden on my back porch and it looks as though my tomatoes are suffering bottom rot just as they did last year. I was under the impression this was due to over watering / poor drainage last year so made an effort to improve drainage in my pots this year by adding rocks to the bottom, making sure the drainage holes were clear and being careful not to over water... now I'm suspecting it's a lack of calcium and that I should have added compost to the soil and used mulch? The fruit is still very young and there are some tomatoes that still look ok and/or have barely started growing... is there anything I can do at this point? If it's hopeless, what should I be sure to correct next year when I try AGAIN to grow some stinken tomatoes... If it matters, I'm in Boston and they're patio tomatoes. Thanks for your help!!
Neato tree bark

Neato tree bark

Flower Pictures

Flower Pictures

Filbert Step (San Francisco)

Filbert Step (San Francisco)

Paperwhites

Paperwhites

Please tell me this could be the work of squirrels.

Please tell me this could be the work of squirrels.

Fun with Weeding

Fun with Weeding