If the seeds inside an apple are brown, the apple is ripe. Pick a few test apples and cut them open; if the seeds are brown you can begin harvesting. If the seeds are still white or tan, the apples are underripe--though you can still use them for apple pie! Apple varieties differ in their tartness, but red and golden delicious should be crisp and slightly tart in flavor.
Don't worry about separating these plants. The only concern is if you plan to save seed for planting next year. Cross pollination does not affect the current year's fruits--only the seeds. (This might be a concern if, say, you were planning to harvest pumpkin seeds for roasting.) However, if you compost the plants and some of the seeds sprout, you could have some strange gourd/squash mutants growing out of the compost pile! But there's no need to worry about this year's crop.