aslan, you might want to take a good look at the description of the electric system of your particular aircraft. This should be in the POH. As others have said, there are several locations where an ammeter can be inserted in the electric system and the exact location differs from airplane to airplane. Furthermore, there are other indicators spread out through the system that you have to keep an eye on, and know what they're supposed to be indicating.
After all, you have three major components that can have current flowing between them: the alternator, the battery and the rest of the electric system (and this all could be split over several buses, to be precise). If you only have one ammeter, it could theoretically be placed in at least three locations. So with a single ammeter you will never be able to get a full picture of what your electric system is doing. You will always need to combine this with, for instance, the low voltage light or the alternator failure indicator to understand what's going on.
In the POH of the PA-28-161 Cadet (issued Sep 9, 1988), I found the following:
As installed, the ammeter does not show battery discharge; rather, it indicates the electrical load on the alternator in amperes. With all the electrical equipment off and the battery master and alternator switches on, the ammeter will indicate the charging rate of the battery. As each electrical unit is switched on, the ammeter will indicate the total ampere draw of all units including the battery.
So if everything is correct then in the cruise the 40 amps consumed by the electric system is totally supplied by the alternator since the battery is, and remains, full. (Although the PA28 POH suggests that keeping the battery topped off will consume about 2A anyway.)
But more likely what you will actually see is that right after starting the current is higher than 40 amps. The excess is used to top off the battery, which was drained during pre-engine-start actions and the engine start itself. After a few minutes the battery is topped off and the current drops to 40.