To make entropy control into magic... What about a universe made of ternary pieces of information?
1, 0, and 0.5 with the middle being entropy and the extremes being inverse information. If you manipulate entropy then you're subtracting or adding 0.5 to your piece of information (but only as long as it stays on the 0 side). To us "1-siders" a 0.5 is representationally a zero since it's the entropy point on our axis. If we assume that 0.5 and 0 appear equal (0 is information that doesn't apply to our "1-sider axis"). Then you can hide magic in the 0 side. If you construct an information blob in 0's and entropy (0.5's) then when you add information evenly to the blob it flips to 1's and entropy (0.5's). Scientific laws stay the same because to the 1's side entropy and "0 information" are identical. You can't read 0 information unless your performing magic. It's always "lost". So now you have the choice of whether you want (real life) entropy to be destroyed information or just shifted to the 0 & 0.5 encoding. If it's lost then you can't push 0.5 to 0 unless you're performing magic. Regardless, you can have another world hiding in the 0-side and you can even constrain yourself to just "producing entropy" and still perform magic: If you only subtract 0.5 from pieces of 1-information/entropy and construct a gradient in potential then when the potential flows it creates energy. Usable energy is information. Anything with structure and direction is information and usable energy definitely has direction. If your 1-side works on 1 and 0.5 values then energy flow is a flow of information that adds 0.5 to whatever it crosses (subtracting 0.5 from 1 wherever the energy was generated (this is your heat production, etc.)). As the energy flows over your special configuration it activates it and makes it real information. You could also have the 0-side act like 1-side information but be indistinguishable and get up to shenanigans that way.
Semi-Clarification (It's still a fuzzy idea):
When we're working with binary states entropy isn't a 1 or a 0. Its definition is instead related to the amount of information we can hold versus how much we're actually holding. Same is true for a ternary state. The catch here is that we only have access and effects from two states. We basically have 1 and +0 and -0. With no way to tell if a zero is negative or not. We've altered entropy's definition here. Since no information actually ever becomes entropy in actuality. It appears as if its entropy whenever there's a 0. That's because each "bit" doesn't store 2 pieces of information, it stores 3. But we can only access the 1 and 0 difference so we can only read 2 pieces of information. We "lose" 1 piece whenever it goes to 0. The definition of entropy here has shifted towards defining any 0 as a piece of entropy. This model assumes information is never created or destroyed. Just rearranged, hidden, and unhidden.
How about the standard illustration about 2 gasses in a container that mix after a partition is removed? How is it made of 0,.5,1 values, and how does adding 0.5 make the gas mix or unmix?
I'm going to move to a lattice model of the universe with information describing the system. Let's assume momentum as a primary quantity. Vector is in a 1, +0 representation. Move it into a +0,-0 representation (add entropy). You've killed momentum but saved state. Manipulate as needed. In the example we need an incoming momentum of (0.5,0.5,0.5) (which is physically none) to reverse our process. That momentum is the same physically as (0,0,0) but informationally is different. Can we add that from nowhere? Physically that's creating energy and reducing entropy from adding two pieces of entropy. If that's not acceptable you'd need to set it up so that when the area outside of our manipulation adds in its quantities we have a vector set up so that the result is our inverted vector which also adds in the possibility of nearby magic messing with us.
Example: (1,0.5,1) -> (0.5,0,0.5) -> (0,0.5,0) + (0.5,0.5,0.5) = (0.5,1,0.5)
The example "inverts" the vector after moving it into "entropy land". You could also just subtract (0.5,0,0.5) twice. When added momentum influences that region it will be in the form of 1 and +0 (remember +0 is code for 0.5).
Note that our "vector" isn't truly "inverted" momentum-wise, we have no negative quantities as described. The above is also a toy thought experiment because I'm not sure what happens when a "1.5" would appear (It can't happen because the ternary system doesn't allow it. A 1.5 is really 0 with overflow of 0.5. Does that excess disappear, propagate to the next cell, is it disallowed from happening, or do something else?)
That's why this answer was meant to be a comment. The system needs to fleshed out and can be tackled in many different ways, all with unique methods of manipulation to cause certain effects. You also need to state what your primary quanta are and describe them. If its a simulation on a machine that's fairly easy. Just take your bits of RAM and make them tri-state. Your program becomes the description.