I found the problem. I have two electric fans that turn on about 15 seconds after the car starts and it was drawing all the volts. I unplugged them and the volts shot up to 13.5 at idle. Now that I fixed that problem, no to fix the fan problem!
If your electrical system is stock, you really need to do the bypass Brad suggested. Those electric fans will likely melt your bulkhead connector.
You can leave it on indefinitely, but your ammeter will not really be giving you an accurate representation of current flow (not really a concern).
Any voltage drop is an indication of a less than perfect electrical connection. The high draw of your fans will make it worse and worse over time due to heating/cooling of those connections. IMO, take your bulkhead connectors apart and make sure they are clean and tight, same for the connector on the passenger side valve cover and the connections on your ammeter (if you still have). Disconnect the battery b4 checking the ammeter nuts - tooo easy to short out in the tight confines under the dash.