Never let them stand in water. That will drown them. Ironically, over watering makes them turn yellow and look like they need more water or fertilizer. Top watering is fine as long as you are giving them enough to soak all the way down and drip out the bottom a little. If the soil isn't soaked all the way down the roots won't grow down. The biggest down side of top watering is that it may flatten tiny seedlings. Once they get to 2-3 weeks old and get a little size to them I water from the top now and then. It helps toughen up the plants stems and get them ready for rain and life in the real world.
I water like Bob does but used a scaled up version. My greenhouse is built with benches I can flood and water from the bottom up. I can do dozens of trays at a time that way. I only water when the soil on top starts to appear a little dry. A good starting soil should wick the water from the bottom up to the top and make it look moist in about a 1/2 or less. Once the soil is moist again I drain the water out. I have 3/8 inch wood slats in the bottom of my benches to keep the trays off the bottom a little. When the bench is drained the flats are not in the water at all, but there is still a small layer of water under them. That helps keep an even humidity near the plants and provides a more even temperature layer below them. And it makes a good habitat for the little frogs that always find their way into the greenhouse. They are natures way of aphid and bug control. Plus I like frogs. lol They never hurt anything.
I use Miracle Grow all purpose fertilizer mixed like it says on the box. I don't use fertilizer until week 3 or 4. Then I use it about every other watering on tobaccos. I fertilize every watering with tomatoes. A good potting mix will have all the nutrients the plants need for the first few weeks. If you really want to make it easy, use one of these.
https://www.amazon.com/Miracle-Gro-...Y3HMXHV/ref=pd_lpo_1?pd_rd_i=B06Y3HMXHV&psc=1 Makes it all stupid simple. No mixing, no thinking required. One pack of fertilizer will make about 40 gallons of water.
I never clip my plants. Never saw a need to do it and I don't have the time to fuss with them all. But is doesn't hurt to do it if you want too. To each his own. And personally I hate peat pots. They don't work well for bottom watering and you must tear away any part of the pot that is above ground when planting out or they act like a wick and suck the water away to the air. The peat below ground never stays wet enough for the roots to grow through them. Also, I have planted out tobaccos that were started in 128 hole plug trays, 4 packs, 6 packs and 4 inch pots. The bigger the pot, the bigger the plant at planting time. But a month later there is no difference between them. The only advantage of a bigger pot is a bigger plant going into the field that can stand up to weather a little better and birds pecking on them. All I use now days is 6 packs. I seed right into them and the plants stay in them until planting day.
Today is the day I seed my tobaccos. 8 weeks to my last frost date. Those of us in the northern tier are always last. Lots to do today so it's back to work now.
Cheers