Living in an apartment makes some aspects of Bonsai difficult, but I may have the opportunity to plant a couple of my not so developed trees into the ground. (long story on how that happened, not that important) is there anything that I should pay special attention to? especially when I can put them in the groud? and how a prepare for taking them back out again?

If they are in pots and you don't disturb the roots much you can do it almost anytime. Prepare the hole with some good compost and water in well.

If I want to take them out again in say.. 5 years.. or longer, is there any way I can prepare the roots so that it is easier to dig them out again?

You could lift them after 2 or 3 years and cut the tap root off.

For me the safest way of digging up a tree is to make a trench around the base (it must have a circumference 5 to 6 times the circumference of the trunk of the tree) cut all roots exposed in the trench, then replant the tree and go back in a year's time and dig it up

Make sure that when you plant your trees, none of the roots are tangles up. You want each root to spread out in its own space. Otherwise you will have a useless tree in 5 years with twisted roots and bad nebari. Check every 2 to 4 years what the roots do, ensuring they grow evenly.