When using an Necromancer's alter from outside of an ayleid ruin and a soul gem to enchant a weapon how can you determine its affects or is it much easy to use an enchanting alter/stand to enchant.

You can't enchant anything with a necromancer's altar. Those are just used to create black soul gems. What effects you can enchant with depend on what spells you have and are capable of casting. Using sigil stones is the only (vanilla) way to enchant something without an altar, and the effects of each stone are listed when you select/highlight them in your inventory. For more on enchanting, look here: http://www.uesp.net/wiki/Oblivion:Enchanting