Let's talk.
First I don't think that
char cmd[] = "C:\Users\%user%\AppData\Local\Programs\Python\Python37" "C:\Program Files (x86)\tool\tool.py";
does what you think it does. When you put two strings like that together the compiler treats it as one long string and you will not get a space between the "...Python37" and "C:...". Better to just make that one string and put your space delimiter in.
For example:
char cmd[] = "C:\Users\%user%\AppData\Local\Programs\Python\Python37 C:\Program Files (x86)\tool\tool.py";
The next issue is that C strings reserve the '\' (back-slash) character as an "escape" character. There's a history lesson in that terminology but that's for another day. The important part is that it allows you to put characters into strings that you would not normally be able to. Examples are things like tabs (\t), newlines (\n), etc. Whenever the compilers sees a "\" it will be expecting another character to complete the "escape sequence". If you actually want a backslash you have to put in two.
For example:
char cmd[] = "C:\\Users\\%user%\\AppData\\Local\\Programs\\Python\\Python37 C:\\Program Files (x86)\\tool\\tool.py";
Next, you are using an environment variable expansion "%user%". I assume that is defined in your environment (it isn't in mine). You need to be mindful of the environment and you may want to check that things are expanding as you expect. One easy way to do this is using your same code but a different cmd string:
For example:
char cmd[] = "echo %USER% >c:\\mydir\\myoutput";
system(cmd);
It's useful to put a full path on the redirect to make sure it ends up where you expect it to. Again I'm going to assume that %USER% is correctly defined in your environment.
Next, you are referencing a file path that has a space in it. That might be why you tried to use the quotes the way you did, but in this case that doesn't help you. The system function accepts a string and for the most part doesn't much care what it is. You need something to indicate that the space is part of the file path. This is where those back-slashes can really help you.
For example:
char cmd[] = "C:\\Windows\\system32\\cmd.exe /K dir \"C:\\Program Files (x86)\"";
system(cmd);
That should open a DOS/CMD window on your desktop, execute a dir of "C:\Program Files (x86)" then leave the cmd shell open. Sometimes leaving the shell open in this way can be handy to see what the default env is.
So putting it altogether your program should look something like this:
int main() {
char cmd[] = "C:\\Users\\%user%\\AppData\\Local\\Programs\\Python\\Python37 \"C:\\Program Files (x86)\\tool\\tool.py\"";
system(cmd);
}