What level are you? I played a True Necromancer (from the "Libris Mortis", think Mystic Theurge but focused on Necromancy) and in my experience Illusion and Enchantment magic, Bluff, and Stealth are invaluable. When you want to retrieve your corpses go under the cover of night and Stealth into the cemetary, use suggestion or charm spells to help convince anyone in the cemetary to leave, and start digging. Zombies can be hidden in extra dimensional spaces like a Bag of Holding or portable hole, Skeletons need to have their claws covered to go in the Bag of Holding. Control Undead can get you stronger minions. Illusion and Bluff can cover your tracks when discovered. Also there is a spell in I think Ultimate Magic called Disguise Other that might temporarily hide your undead from potential mob starters. I used Veil, but that might be too high a level for you. The one time I got caught was when I got called into town by a sending mid animation and used Hallucinatory Terrain to cover the hole and a little girl fell into her fathers grave with the pile of flesh that was her father next to his skeleton who was instructed not to move. After returning I helped her out of the hole but she ran and started a mob (figures). I stealthed into town and heard the girl tell her uncle about the mess so I used Disguise Self and dressed up as a cleric and went in. I was Chaotic Neutral so I could cast good spells and offered to cast Hallow on the cemetary. My party members kept the mob from stepping through the illusion and into the graves so I cast the spell and used diplomacy to disband the mob. They actually thanked me as they left. So once everyone was gone I got my 2 skeletons (yes all this for just 2) and filled the holes back in. They were fresh graves to begin with so no one really noticed that they had recently been redug. To avoid this fuss you might just want to animate your fallen enemies and hide them as above. Sorry the post is so long but I figured it would give some insight into possible ways to deal with the mob.