Hi Lauren,
For gift cards it is more manual management, because POS does not require customer ID when using/issuing gift card.
The way to see to which customer gift card belongs to - is to check gift card history 'Invoice account' field - for 'issue' operation customer ID will be there.
In POS: if you have 2 programs assigned to 1 loyalty card, both of them will be used when you scan the card. If you use 2 loyalty cards - you can split programs to these cards, so programs will vary depending on what you scan in POS.
I do not see standard function to update all loyalty cards at once, but it is possible via Extension (on F&O side, not POS)