firstly, you should seperate them on the basis of plant type, ie legumes (peas/beans), brassicas, roots, onion family, and grow each one in a different place each year. This is the principle of crop rotation (in this case a form of 'four course' rotation). the change in location each year reduces the likelyhood of a build up of pests or desiese, and helps prevent the soil becoming deficient in a specific nutrient. For example a plant type that uses a lot of nitrogen may be followed by legumes, that 'fix' atmospheric nitrogen and so take little from the soil. This doesnt mean you dont have to fertilize, but helps balance the nutrients.
secondly, organise where you put things on the basis of how fast they grow, how big, and your need to access them. If you grow your peas in the middle of your carrots, it'l be difficult to pick them without standing on the carrots! grow fast maturing plants (radish, lettuce) intersperced with slow growers. They will provide protection over them and increase your productivity. A fast plant will also help mark the row where the slow ones are!
There is some evidence that growing certain plants alongside others reduces pest problems, such as growing marigolds along with carrots. The idea is that the stronger scent of the 'companian' plant masks that of the main crop, and makes it difficult for the pest to locate. I will be planting marigolds around the edges of my carrot rows to try and deter carrot fly.
hopefully thats a good background for you - now prepare for a mass of advice from everyone else (all most likely very good, i will point out)