Ground is simply whatever is connected to the chassis, it can be positive or negative, just happens to be negative in most cases these days.
By no means hook an amp meter across the battery, that's called a direct short and will yield nasty results. You WOULD do that with a volt meter.
An ammetter on a car or whatever is set up to read what the alternator is putting out to the battery. You wouldn't really want it in series with the starter cable since that will abuse the hell out of the meter. Putting it in the first location will tell you if and how much your system is putting out.
So it needs to be connected in series with whatever wire runs from the alternator output to the positive of the battery on (negative ground applications) or from the alternator output to the negative terminal of the battery on positive ground applications.
Polarity of a DC amp meter matters, hook up it up backwards on a DC circuit and it will pull the needle in the wrong direction. Probably won't damage it unless it bends or eff's up the movement but a good meter ought to be tougher than that.
One way to confirm your polarity is to start it if you can and put a volt meter across the alternator frame and the alternator output lead.
The alt. should be putting out negative since it's case grounded to a positive referenced chassis. Since the case of the alt. is the other side of the circuit and it's positive grnd system it pretty much has to be negative output to work
Any reference to positve or negative when using a handheld meter requires that the red and black leads of the hand held meter be on the proper spot, which isn't an issue when measuring AC. If the leads aren't hooked up and used right then the - Or + on the meter display means nothing.
I would hook the negative of your mounted ammeter up to the alternator side of the circuit and the positve to wherever that wire goes.
True your actually hooking the meter to a negative output lead and a wire that leads to a neg batt terminal but the current flow is from positve to negative and in that respect the source of your negative is the alt. so your battery neg term. gets the positve lead as positive polarity is coming from the positive term. on the battery, through the battery and then out the negative term.
For this to work you have to completely interrupt/break the output circuit and send all that current thru your meter, you can't hook it up in parrallel with it or it won't read all the current. (two paths)
Whatever the case simply hook it up in series with the alternator output to the battery and if it reads backwards then simply reverse the connection.
In the event you are dealing with an older style alt. with a separate diode pack or R/R as we call it on the Vmax (this is the arrangement on the Vmax, i.e. AC generator with an AC output going to the R/R then DC from there) any references I made to alt output would apply to the diode pack or R/R output instead since that's the DC side of the circuit.
If it's old enough to have a positve grounded system then it also probably has a separate R/R instead of the diode/R/R pack being built in to the alternator like on modern automobiles.
You could also have a system that uses a generator with a direct DC output, these suck since the voltage output is based on RPM, and may use some sort of regulator to stabilize DC output but it won't be the diode pack used to turn AC into DC. it will be a Zener diode that simply bleeds off excess voltage above a certain limit, which a normal R/R also has in addition to the rectifier diodes it uses.
You can still hook your meter up in series with this but it's gonna drive you nuts looking at it since it's going to be all over the place since votage is going to be changing with rpm and consequently effects the current too.
Your best bet in my opinion is to use a voltmeter instead, it will tell you plenty about your system condition since if the tractor is consuming power and your charging system isn't keeping up you'll see your voltage levels dropping anyway. It just takes slightly longer since the battery has to deplete before a tits up charging system will show up on the volt meter.
Even better is to install a modern alternator with a built in R/R and convert the whole thing to negative ground, but it would require getting a different starter, or having your starter re-wired/wound for a negative ground. As well as a few other items that would need addressing. I don't think your lighting would need any attention since resistive elements like light bulbs are not polarity sensitive.
Clear as mud???