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First, you can only access the bank you are currently running in. Normally this is slot0, but you can change that with the RUN command.
As for multiple serin/serouts, it's perfectly legal. However, if you write your code well, you don't need more than one of each. Truly, you don't.
You are correct that the program starts from the bottom and builds up. If you want to put data into the top portion, there are a couple of ways to do it:
1. use the DATA command. This will load data into EEPROM when you first send the program to the RC. Useful for tables, etc.
2. use the WRITE command. This will let you change an EEPROM location at run-time.
Be warned, however, that the life cycle of an EEPROM location is only ~100k writes. At 40 loops/sec, this gives approx. 41 minutes of runtime before you can no longer use that particular location. If you have less than 64 bytes of data to store, use scratchpad RAM instead as it has unlimited reads and writes. The PUT and GET command let you access this.
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