When you plant the peat pots, make sure the rims are not sticking above the surface of the soil. The peat can wick moisture away from the plant if any of it is sticking up. You can tear or cut away the top rim.
It's a good idea to water the plants before transplanting them, so that the soil will hold together better. You want to transfer as much soil as possible with the plants. Ideally, the roots will be holding the soil mass together when the plant is ready to transplant. Some plants do not like having their roots disturbed, so for them it's best to keep the soil mass as intact as possible. Cucumbers, squashes, and other plants in that family do best if their roots are not disturbed. (So the advice is usually to plant them directly in the ground, not in pots. I've done both and prefer planting in containers where I can keep an eye on them.) Other plants are very resilient and will quickly replace any broken roots -- tomatoes in particular can recover from nearly any injury.
Depth depends on the plant. Plant tomatoes so that only the top 2-3 pairs of leaves are above the surface of the soil. Gently remove any leaves that would be below ground. You can dig a hole to plant them deeply, or else dig a trench and lay the plant sideways in the trench and then cover with a few inches of soil. The plant will grow upward on its own. It will also grow roots along the part of the stem that's underground, making a stronger plant. Other plants in the same family can be treated similarly -- peppers, potatoes, eggplant -- though it's most important to plant deeply for tomatoes.
An old fork or spoon is a good tool for scooping transplants out of flat trays. Again, you want to make sure to get the whole root mass, so scoop out as much soil as you can.
If you have a mass of tangled roots and want to separate the plants, first you have to make sure that it's a plant that can withstand some root disturbance. If it can, the easiest method is to get a pail of water, take the plants out of the container, hold onto the green part, and swish the rootball around in the water to loosen the soil. Then, under water, carefully tease one plant at a time away from the root mass, starting at an outer edge. Doing this under water helps the roots to slide apart more easily. Cover the roots as you separate each plant so that the roots are not exposed to air and sun. (Then, if you're called away in the middle of the job, you won't return to a pile of dead plants.) I've separated a thick block of seedlings successfully using this method with plants in the onion family -- it's a great way to get 50 or so plants out of one 6-pack!
It's always a good idea to prepare the planting holes before removing plants from their pots. You never want to leave plant roots exposed to air and sun for more than the time it takes to move them from the pot to their final hole -- the air and sun can dry out and kill those roots very fast! So you need to plan where you will plant each seedling, make the planting hole, make a label so that you know what you planted where, and only then remove that plant from the pot -- one plant at a time.
Once your plants are planted, water them in well. I like to water not only the individual plants, but also the area where I want the roots to grow, usually a circle around the seedling extending several inches. Many plants stay healthier if you don't get water on their leaves: tomatoes, cucumbers, squashes. Keep the seedlings well watered for their first few weeks so that they will develop strong root systems. You can stick a finger in the ground a few inches deep to make sure that the water is being absorbed. If the soil is still dry, water more; if the water is running off, water more slowly.
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