Simulator and the Ports

I will be travelling July and August and would like to take this respite to generate some code for future projects. I found that building the hardware first makes for difficult software design. I’m using a Mega 2560 to control an array of 16 bit input and output memory boards. On the Mega 2560 pins 14 - 21 are used for the address. Pins 22 - 37 are for Input, and 38 - 53 are for output. I would like to use the included simulator to perform some initial debugging on the code as dragging the hardware along is just not feasible. It appears that you can simulate external hardware by manually adjusting port values (I’d just be adjusting address and input pins) while observing Output ports.

The problem I see is that the Ports are assigned pins in an almost random manor while related input/output data are grouped onto one of the external boards. This makes it very difficult to track what’s going on and can lead to errors… Is there any way to rearrange or otherwise make some sense of the port - pin relationship.

What included simulator?

Use the ports anyway, and if the Mega doesn't map complete ports out to hardware pins, there are other hardware solutions that will let you use full ports, example, one of my designs: