I'll try to explain...
Somewhat similar to, say, football each pick in the MLB draft is assigned a certain signing bonus. But unlike football, a player drafted with that pick doesn't automatically get that signing bonus. Instead the slot amounts of all the picks a team has in the first 10 rounds are added up together and then can be distributed among the drafted players however the team sees fit.
Very simplified example:
It's important to understand that teams usually negotiate signing bonuses with players before they draft them, not the other way around.
So, let's say our team has three picks with the slot values $3M, $2M and $1M, meaning they can spend $6M in signing bonuses total on their draft class. Of course they could just hand it out like that.
But maybe don't like the consensus top players for their first pick and draft someone lower on the board who they found out is willing to sign for only $2M. They now have $4M for their other two picks.
Meanwhile, there are always some players in every draft who fall because no team is willing to meet their asking price. Often HS players who have the leverage that they can just decline and go to college.
Since we "saved" money with our first pick, we now have more left than most other teams, $4M, and can just go to one of those should-have-been first-rounders in the second round and throw first-round money (e.g. $3M) at them.
So, to sum up, instead of getting a first and a second, we ended up with a slightly worse first-rounder and another guy that should've been a late first. It's basically baseball's version of a trade down, except that the actual picks are never traded.
Like with the Mets, it can work the other way, too. Maybe in my example the team really likes a player expected to go before they pick. So they go to that player and offer him $4M to sign. If that player then communicates to the other team that he won't sign for less than $4M and no one else is willing to give that to him, they might let this player slide right to our team. Of course, that also leaves only $2M for the other picks, meaning that we'll have to use our second-rounder on a player that's not really worthy of a second-round pick but doesn't have better offers from other teams. That scenario would basically be a trade up.
I hope that helps a bit? I agree, the MLB draft can be confusing to watch, especially because fans don't know those prenegotiated deals until the players actually sign a month or so later.