Young plumeria branches have some sort of fungus?
It could be powdery mildew, which is a very common fungal disease.
Here are steps to prevent and control it:
https://www.gardeningknowhow.com/plant-problems/disease/get-the-cure-for-powdery-mildew.htm
A few branches on my plumeria plant have some soft spongy areas up toward the flowers. What is this? What can I do to help the plant? I don’t over water the plant and always from the bottom of the plant not on the flowers.
It looks like a fungal issue, likely verticulim wilt. This is caused by overly wet soil, or watering too often without letting it dry out thoroughly down to 3 or 4 inches for this plant. They will not tolerate wet roots without a good dry out between each watering.
This will have to be treated with a fungicide. This article will help: https://www.gardeningknowhow.com/garden-how-to/info/using-fungicides-in-garden.htm
It would also be beneficial to put a tablespoon of dolomitic lime and a teaspoon of wettable sulfur around the root zone. This will help to remove the infection from the soil. Do this once or twice per year for added protection.
This article will help you with the general care of the plant: https://www.gardeningknowhow.com/ornamental/flowers/plumeria/growing-plumeria.htm
the bottom. Should I just plant it?
Here is the correct method for rooting cuttings: https://www.gardeningknowhow.com/ornamental/trees/tgen/how-to-root-cuttings-from-various-shrubs-bushes-and-trees.htm
I love them but they’re taking over the side of my house. I have two trees that are quite large, and I want to know how to trim them without killing them. but I need them not to grow into my gutter in my house.
This article should help:
https://www.gardeningknowhow.com/ornamental/flowers/plumeria/plumeria-pruning-info.htm
My Plumeria has black spots on the bottom leaves. Top leaves look good. What do I do?
This is a common issue caused by overwatering. Usually, making the soil more acidic with Wettable Sulfur will take care of the issue, both, in killing off the culprit responsible, and bringing the soil pH back down to where it needs to be. They tend to like acidic soil.
If you water by hand, or provide any extra water at all outside of natural rain, then make sure you only do this when the top 2 or 3 inches of soil is completely dry before watering again.
This article will give you more information on the care requirements of the plant: https://www.gardeningknowhow.com/ornamental/flowers/plumeria/growing-plumeria.htm
I live in southern California. A month ago, the leaves began curling. I believed it was an insect issue and sprayed them twice with Bayer 3 in1 insecticide. Now, the leaves are black and yellow. Please see attachments. I have also sprayed them a sulphur based fungacide. I am worried because it seems like this issue has spread to all of my plumerias. Thank you for any advice you can give me,
It could be plumeria rust. Look on the underside of the leaf for rust looking spots. check below for approved fungicides. Be sure to pick up fallen leaves and destroy.
the foliage is healthy is free of disease because I use baking soda spray. Should I leave it in its 12 inch pot?
Yes, I would leave it in its pot. That doesn't sound too small. Give it a good spray of water to knock off any pests before bringing it in.
Plumerias are hardy to zone 9 but since it is so small, I wouldn't take any chances; plus you can have below freezing weather in zone 9 and 10, which they don't like.
https://www.gardeningknowhow.com/ornamental/flowers/plumeria/growing-plumeria-plants-indoors.htm