Can you be a little more specific on what you're wanting to do?
If, by two "systems" you mean the city where you work is in, say, the digital TxWarn system, and where you live is on the analog system, then that would be two separate downloads of system information into scanner software. On the other hand, if both locations are on the same system, but just covered by different transmitter sites, then you could download all the necessary information at one time, but you'd need to be sure you entered it correctly in your scanner.
How about which cities, and systems, are you talking about, and which scanner? That would help getting you a more complete answer.