It depends on what your post processor file tells the CNC to do between tool changes. If you don’t have X,Y and Z end stops or some easy to locate origin then you need to have all tool paths in one gcode file and have the steppers locked between tool changes. I don’t bother with ends stops.
I use Fusion 360 and a MPCNC specific post processor http://www.vicious1.com/forum/topic/fusion-360/#post-4237 that pauses between tool paths. It pauses, displays “Change tool” on my LCD, moves to a location near the origin that gives me space to get the bit out, and most importantly it keeps the steppers locked(powered) and disables the normal 1 minute timeout on a stepper lock. This way I can carefully change the bit without the axes losing their place. I then just resume and it starts milling the next tool path. See this example http://www.vicious1.com/forum/topic/cosx2y2-milled-in-wood-post-1/ where I changed from an 1/8″ end mill for the outline and roughing to an 1/8″ ball mill for finishing. I just make my origin at one corner of the stock. It works great. I have not used Estlcam so I’m not sure how to control tool changes for it.
Does this make sense?