Hi Welcome to Mobiflight.
All Users here include myself was "green" when we startup with Cockpitbuilding..... So thats normal.
Please Note....Those Information are also puplished in the FAQ Section or you can find out by using SEARCH and GOOGLE.
About Question:
Mobiflight can run only in ONE instance on your PC ....In Adanced Cockpits you can build a Network ( With the WideFS Programm of FSUIPC) .... Then on every Computer in Network that include WideFS Client you can also run a adittional instance of Mobiflight...
. BUT that is basicly not needed and only for verry large and complex cockpits.
So starting MF two times on a Computer is NOT POSSIBLE !
Mobiflight can handle theoretical unlimmeted number of Megas ( Whatever Windows itself have a limit of 128 as i know) . So a System with 10, 20 or more MEGAS is possible on ONE Computer and with only ONE "Mobiflight Connector"
You can use Up to 52 Pins ( Only Pin 0 and Pin 1 are NOT for personal usage) .... And you can Mix your devices within the Limits ( For example 40 LED Max on a Board.... Or 20 Encoder Max on a board and so on) Information is listed in the FAQ section.
So for example 30 Buttons and 20 LED together is Possible on ONE Mega Board.
Summary.... If you have free pins on your Mega you can include the Flaps part... If Pins are full simply connect the next MEGA Board and you can going on . ALL is done with only one Mobiflight Connector !
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Last Note for beginners....
I Recommend to "learn" at first before you start building.
Take your board and set for example 20 LED and 20 Buttons.
Then Make your Gear System. If it work SAVE the config file and open a empty new one.
Now Build your Flaps system with the SAME Hardware ( Without gear). If it also work Save it again in a other file and start again with empty file and test the next one (for example Autopilot controlls)
On Beginning you will make a lot of Mistakes. Big issues can "kill" your Config file. So its recommend to make your final file (You will use with your real Hardware) when you realy know what you do and you still know your config is correct.
Those "Sandbox testings" is the best way to understand the basics !