Answer: Seedlings normally grow at their own correct level, so you should not need to adjust it for them.
There are two reasons I can think of why perennials would raise themselves up. Some perennials will "heave" or be lifted a bit above their preferred level in the spring or fall due to the ground freezing and thawing and the pressure forcing them upward. When this happens, their roots become exposed seemingly overnight and should be pushed back into the soil when the ground is soft enough to allow you to do it -- usually on the next warmish day. To reduce the occurrence of this frost heaving, make sure the soil is well drained by adding ample amounts of organic matter and possibly a bit of sand, and in an area with very heavy soil you might consider using slightly raised beds. Maintaining a layer of organic mulch such as shredded bark over the roots (but not covering the crowns as this will encourage rot) can also help reduce freezing and thawing action.
The second reason is improper planting, so that the surrounding soil settles and leaves the rootball at a higher level. When you plant, dig a generous hole and back fill carefully, settle the plant into the hole by wiggling it a little and firm the soil as you go so that it will not settle excessively. Firm it well when you have finished filling in the hole and add more as needed. You should be returning nearly all of the soil to the hole that you took out. Water the plant in well, and then make sure that the soil level around the plant is the same as it was when it grew in the pot or possibly about a quarter inch deeper, just barely enough to cover the soil the plant came in. This should avoid the problem of excessively settling soil -- an effect that will worsen every time it rains if the plant was not planted right.
It is always a good idea to remove decaying or dried foliage, or dead leaves. Sanitation can be important in controlling any diseases that might develop and can help reduce insect problems. It also helps the plants to look tidier in the garden. In most cases you should not be seeing a lot of dead or wilting foliage during the growing season. If you are, there is probably an underlying reason such as insects or a fungal infection or either over or underwatering. Examine your plants closely for problems if you notice something amiss.
Pansies may normally brown when the weather turns hot, especially if they have grown a lot and are crowded in their pots. This is due to both heat and/or water stress. Pansies grow best in cool weather and may exhaust themselves by the time the weather turns hot. In some cases moving the pots to an area with morning sun only rather than sun all day can help them withstand the summer heat and continue blooming, or at least hold on until the cooler weather of fall when they will start blooming again. Since they look so ratty in hot weather, many gardeners treat them like cool season annuals and throw them out when they start to look bad. Cutting them back, fertilizing and making sure the soil is evenly moist but not soaking wet may help. Also be sure to keep the spent flowers removed so that the plant directs its energy to blooming rather than trying to make seed. Planting them in the ground may help since the soil will stay cooler than it would in a pot, but at the same time it is stressful for the plants to have to prodice new roots this late in the season. You mgiht try it with some and see what happens.
In my experience, pansies are best replaced at least annually, although in an ideal climate they might last a little longer.
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