If you stick with Blender you will learn the necessary key functions, and with functions I mean their shortcuts, too. I've been using it for geological modelling which had it's downsides because Blender gives you some trouble with pure point and line objects - they mightbecome invisible in object mode which is annoying if you compare stuff. But in the end, everything went fine!
For a static map you can also ose ply which is originally meant for 3D x-ray scans but the file format is as easy as obj and it is more direction safe. obj-files are often thought to switch between the horizontally y- and the vertical z-axis which can lead to weird results. The real difference in usage for ply and obj is that obj is easier to give whole faces certain colors while ply makes efficient use of vertex coloring. Vertex coloring allows for easy applicable color gradients between vertices and a smooth appearence. However, as game programmer you might be better off with obj because it is meant for such purposes and, despite being not sure, I think ply does not support textures/texture coordinates.
Blender allows you to display vertex coordinates in the 3D-window. This helps. You can further position every vertex by its coordinates. Make use of the orthogonal viewport (press num5) to prevent being mislead by the perspective. Utlilize the 3D view direction (num7, num1, num3) and stay alogn the axis as long as possible because you can always move a point along 1 axis only or a plane of 2 axes (pressin x, y, z while manually rotating/translating or combining them with shift? to the planar movement). Use "snapping" when you already have a faces, edges or vertices which you want other objects to be attached to. For more organic/natural models do not hesitate to use "proportional editing" which gives you a tool to move not just one vertex, edge or face but grab somethign and drag the surrounding mesh components, too! This way a key feature for my geological model as it allows to stretch a first assumption of a layer to the actual elevations/positions. Use array modifiers whenever it makes sense, so you don't have to repititively model identical parts of the whole thing. Best example is a high building with balconies, windows, etc. which is actually amde of repedetive parts. Even on a smaller scale (e.g. a fence) you can use array modifiers to accurately position parts of it. Keep your model clean as long as possible. "Remove Doubles" and "Recalculate Normals" because wrong normals and edges at the exactly same position might srew your lighting up afterwards and they steal away some memory. Always keep in mind that you might reuse objects. Give them materials early, so you can easily change every object of the same material easily at the end. Phew, there are a lot more things than I can tell you or I even imagine. I am kind of new to Blender myself but I possibly faces the same problems as you. Read/watch tutorials which actually show you how a house is constructed in blender, or to be more general: a good tutorial should show you the actual model devlopment instead of naming the key presses for some tools. This way you know for sure, that something will work for you.
At the end: Blender is powerful and, besides driving you crazy (especially at the beginning) it can be addicting like programming