Normally if you machine soft jaws in place they fine. I normally load them with a piece of bar stock clamped in the vice below where I am machining them. Using parallels is another option, just stick a piece of paper on top of the parallels at each corner, then tighten the vice, smack the stock with a dead blow hammer as needed to get the stock seated on the parallels. If the paper is tight, it's seated.
If you have any bolt holes in your finished part, then bolting it down to a fixture plate is my prefered method. Clamping to a fixture plate with a Mighty Bite style clamping system or just toe clamps works well also.