Internally, Trainz keeps track of baseboards by ordering them in the order in which they were created, so that, regardless of the location of the second board you place relative to the first, it is the second board. Personally, I keep track of baseboards by using an alpha numeric grid system. If I were planning a large route, I'd assign the first baseboard of a route the designation M100, as in Column M, row 100. Boards in rows with smaller numeric designations (e.g. 87) are below, and those with higher numeric designations (e.g. 142) are above. Letters earlier in the alphabet than "M" are in columns to the left, and those later in the alphabet are to the right.
The exact designation of the first board might vary depending upon the size of the route. If I were planning a mega-route, and intending to let my whim guide where its size and shape, I might start assign the first board "MM500" or even "MMM1000".
As far as during the construction process, you can use features of the geology of the route-in-progress, for example, naming boards for the rivers, hills, mountains, and other geological features they might contain, or in other ways. For example, a baseboard containing a single specimen of a single large tree in a board that otherwise consists of grassland might be called "Tall Tree". Finally, if you have some content creation ability, you can create your own markers.
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