There are programs to simulate Arduino code, but they are very limited. To really simulate the circuit the program would have to also know about the IC you are using. You didn't told us what IC this is, so we can only speculate, that it might not be something, that these programs know (though you can try it). And sometimes Arduino Simulators have problems with simulating time sensitive code. If you want to try, just google for Arduino Simulator and check out the possibilities. I cannot suggest one, since I didn't use one until now.
At this point it might be the better option to write time-keeping code using the
millis() function, which returns the number of milliseconds since the Arduino started. Save a timestamp from when you started and compare the difference between
millis() and your timestamp to the wanted bake time.
You can pack this code in extra functions, that can later be replaced by code managing the "timer IC". With dividing your code this way you can write the rest of the logic without bothering about the timing part (after writing the
millis() part as a "dummy").
For an oven timer the accuracy of the Arduinos clock should be ok, since it doesn't really matter, if it is a few seconds off. And for testing and writing the first code version it is also sufficient.
If the IC you are referring to is a RTC (Real Time Clock) module, the code for it should be pretty simple to write. There are libraries for the most common RTCs. You might want to try the Arduino Time library.