Well without an alternator there is not much to test other than the batteries, charge them up and have them tested either a good parts store or gas station that still does service work. They can bring the tester right out to the Scout and test.
But when you get an alternator you can test the charging circuit, starting with batt voltage with the Scout off then again with it running and check both batteries that way.
You should see 12.5vdc without the truck running and approx. 14.5vdc with it running, again you should see it on both batts.
Also your stock amp gauge should read just like normal when you batt switch is in the stock or batt a position, but if you switch to batt b you dash amp guage will show some discharge but the stock amp guage does not work in the batt b position.
You can do amp readings also but you will need a volt meter that reads dc amps.
Now having said all that did you notice any over-charging before the alt started smoking? I have seen my system go it to an over charging situation just a couple of times since I install the dual batt system. As near as I can tell it is the batt isolator sticking (for a lack of a better term) when it happens I turn the batt switch to off and ground the posts on the isolator just for a second, turn every thing back on and its fine. Just fyi and my install was back in 2010 so this issue has not been a big concern, but I do watch my amp guage a little more than I used to.
Ron