If this is going to be 2D only (meaning all your 2D Sprites will be authored in a static Isometric view), then I'd suggest making a test game something like this:
o Author a simple Player character (ie. 1-frame verticle rectangle).
o Author a simple isometric square building.
o Create a grid of streets with these buildings occupying the areas between streets.
o Work on figuring out how to move your character around this simple layout.
o You can quickly explore techniques for managing InFrontOf/BehindOf situations (ie. Alpha blend the buildings the player is behind, where overlap occurs).
Depending on how complex or simple your layout will ultimately be, you could get away with a simple cell-based approach where objects/buildings/characters/etc occupy certain cells. Collision detection would be a quick matter of "Did player attempt entry of an occupied cell?"
If it's a more complex layout, then like the article previously mentioned (grip & tile) describes a more pixel based approach (simple collision between two 2D sprites), which is again similar to the cell-based approach, but on a finer level of detail.
That Isometric Games Programming site looks like a good starting place. Just keep it simple and build from there.
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