I dont know whether it is time to go into the machine co-ordinates and program co-ordinates, but it ties in with your first question.
You have fitted switches - you don't say where - but I assume that these are combined limit and home switches. There is a difference. If they are acting as limit switches, then, once you have activated them, that should be that - the machine should go up to them and STOP (It has reached it's limit). So that is the first job. Get the switches active. Wire them up to LPTI (or your BOB) one at once, and configure them on Config/Ports and Pins/Inputs. When you have done this turn to the diagnostics page, and (leave the table out of the way) switch the switches manually. You should see the appropriate led light up. If it has already lit, then it is configuraed wrongly, and the active low/high needs changing. It you can't get it to light, then you must look to your BOB. I can't say any more, because a lot of Bobs invert the signal, and there are so many combinations, it is impossible to say, but the right combination of high or low common, low or hign input is there somewhere.
Once the limit switches are fitted, configured and working, then you should be able to jog round your table and when the switches are hit, the table will stop. If you tick Auto Limits on the settings page (or something like that - I am away from my machine at the moment so can't check the proper name) then this will allow you to back off the switch.
Home switches work differently, although they are (in many cases) the same switch. Here the machine will travel (at reduced speed) until it hits the switch. It will back off until the switch opens again, then stop again. The DROs will automatically set to 0 (if you have the homing page configured that way) - end of story - there is nothing else you can do with homing - and you will see from the page, the speed and directions can be specified, so you can home to the most convenient point for you. Mach 3 automatically alters the program when reading a switch as home or limit.
Here is the rub - because with homing you are joining the "big boys". Homing sets your machine co-ordinates to zero. Machine co-ordinates are those by which the machine keeps track of its-self. You cannot alter them, other than to home the axis.
If you press the Machine Co-ordinates button, and the led is lit, then the DROs are displaying machine co-ordinates, if you press the button again and the light goes out, you are viewing program co-ordinates. Program co-ordinates are the method you use to keep track of the machine, because it refers to your program.
Home the machine and check the machine co-ordinates (0.0.0). Press the button and view the program co-ordinates. These may also be 0.0.0. If they are not, then zero them by pressing the zero buttons at the side of the display. Your two systems are now together.
If you now jog you table to where you want the 0.0.0 to be for the program you are running, and when you get there zero the program co-ordinates, then if you check, the machine co-ordinates have not changed. The values displayed on the machine coordinates DRO's are the offset of YOUR 0.0.0 position, to the MACHINE 0.0.0 position, and if you now look at "Config/Fixtures" you will see that G54 reflects this. There are 255 offset slots to use. G54 is the default. If you copy these to G55 or G56 then you have YOUR 0.0.0 referenced.
You can now try for real - home your machine - from anywhere. Type in G55, followed by G0 X0 Y0 Z0 and the machine should now go to where you wanted your 0.0.0 position to be.
If you include G55 at the beginning of any programs, if you "home" your machine, then run, it will always start from exactly the same place.You will see that with 255 slots to go at, your can start your programs from anywhere on your table.
Hood mentioned about telling Mach 3 the size of your table - yes you can set soft limits, which will prevent the machine exceeding these. However there is no way you can tell Mach3 you have a 10 x 12 table or whatever. Mach 3 reads your program, and draws the limits on your toolpath display from your program, therefore you need to keep your program inside the limits. I can see, from your picture that you obviously have limits, from theconstruction of your machine, I on the other hand, can overlap my table, therefore the size is irrelevant.
That seems enough diatribe for a Sunday morning.