The Confederate generals were tactical geniuses, but they sucked or were indifferent to the mundane things like supply and mounting sustained campaigns. Most of the food shortages and medical shortages were due to lack of attention to detail and a corrupt quartermaster corp. No sutlers were allowed in the South and this left to much power in the hands of the supply officers.
In retrospect that was poor planning certainly, but the south nearly attained their original goals. The North was losing it all, and badly, until US Grant came along.
The confederacy never planned a protracted war and that is in fact why the union won. The south simply was worn down by attrition and blockade. The union lost more troops but had the resources to fill the gaps.