Did you receive the plant bare root? Do you know if it had been lifted before you got it? The brownish main stem starts out as a root underground and is best left underground if you want it to continue getting bigger. Ideally you should try to hit a balance where you expose some of it to enjoy the fat-stemmed look, but leave some of it buried, so that the buried part can continue to grow. You need to base your decision on where it was before it was sent to you, unless you've had it potted up for a while. The most conservative move would be to pot it up exactly as it was before, with the part that was previously buried still buried.
Once you lift the stem, or if it was previously lifted before you got it, it's generally best not to rebury it. If it's just been a few days or a week or two, there's still time for a change. Otherwise what's done is done.
It's not obvious on first inspection how the plant actually grows its stem, especially when it comes to you without soil.
It's generally best to avoid watering any succulent Euphorbia right after you pot it up, especially if you were handling the roots or if they experienced some kind of trauma during shipping. The idea is to avoid provoking rot by allowing the below-ground parts time to heal before they are submerged in dirty water. This especially important for plants with underground stems, which are more prone to rot than regular fibrous roots.
If the stem is shriveling, be on the lookout for rot. If it's just a bit underinflated, that's probably because it went for a while without water, and no big deal, because it's reversible. If it's squishy or discolored, those are the warning signs for rot, especially if you can see it progress over time through the stem. Over time you will get a better sense of how your plant responds to care but these are useful general guidelines for now up front.
Wait for the soil to dry out at depth (which might take a week with strong light and warm temperatures) before you contemplate moving the plant or reburying a bit of the exposed stem. When the soil is dry, you can make your move. Just wait a few days to a week afterward to water again, depending on whether the roots/underground stem were damaged during the process of handling.
Try to get it set up so you don't have to unpot or repot again for several months. Winter is when your plant is most at risk for rot, given the lower light and lower temps. Ideally it's best to do the repotting in the spring, once you get your plant in a rhythm.
I hope that makes sense, otherwise let me know and I'll try to clarify.
