If I have a flower-box for plants on top of clay using top soil, would they live?
Clay is rich in nutrients but can bake hard in dry weather causing problems for plant roots. Putting a box of soil on top of the clay would be fine if the soil is deep enough for the roots to develop properly. It would be better to break up the clay and dig in sand or grit and then put the soil box on top. That way you get the best of the nutrients in the clay without the risk of the clay forming a solid barrier to roots
Do perennials bloom once a year?
This depends on the type of perennial you are growing. Some flowering plants only bloom once in the season while others will continue to put out blooms once the dead ones are removed.
I recently filled in a concrete based (approx 12Lx8Wx4 ft deep) pond in and tried to make it a flower garden. Now I fear I have too much moisture as my flowers have black spots on their leaves and moss is growing on the mulch. We started by filling in with about 3 ft of good fill soil, half a foot of good gardening/planting soil and a couple inches of mulch. We have had a lot of rain. It's impossible at this point to dig it up and drill drain holes in the concrete, so is there anything else I can do or plant that will help with too much moisture? Thanks
Possibly a bog garden. check out this article: https://www.gardeningknowhow.com/special/spaces/designing-bog-gardens.htm
Another alternative might be a Corkscrew Willow. You could add some hosta and ferns.
I live in NW PA. Today is Feb. 8 and my spring flowers are coming up early. How can I protect them from the rest of the winter?
Most of your spring flowers, especially bulbs, are considered hardy and accustomed to these conditions. Although they sometimes pop up early under mild winter conditions, there's usually no need to worry if temps drop again. However, if the temperature drops and it makes you feel more at ease, you can cover them with a blanket at night but remove it during the day.
The spent blooms often stay on for weeks so would like to remove them if possible.
Is it better cut back plants in the fall or spring? I live in southeast NE right on the border of zones 4 and 5. I also leave the fall leaves on my flower beds for protection against subzero temperatures. Am I doing any good or not?
While many people prefer to clean up their gardens in the fall, others prefer to do so in spring. This is usually based on preference as well as your regional climate. I would say in your area, leaving some fall leaves in the beds overwinter would be a good idea, as it not only provides insulation during cold periods, but also will eventually break down in the soil.
Also, leaving growth on some of your plants may help with their continued survival over winter. All dead plants (like annuals) can be cleaned up and disposed of. Spring is often the best time for pruning chores (for most plants) but in warm areas can be done in fall as well. Here is an article that you may find helpful: https://www.gardeningknowhow.com/garden-how-to/projects/fall-garden-clean-up.htm
How to design a flower bed for year round interest?
This should help you plant your year round flower beds: https://www.gardeningknowhow.com/special/spaces/designing-four-season-gardens.htm
When you plan your garden, be sure to consider your USDA planting zone: https://www.gardeningknowhow.com/planting-zones/usda-planting-zone-map.htm