Yes, the disorder in my cargo was very annoying too. So I invented t.c.r.-parties.
What you do is sell all your spices, till your cargohold is totally empty. You can also sweep it while you're at it.. Then you do a roundtrip to all the creatures and plants you want to have, and in the order you want to have them. Keep selling that annoying spice they keep adding to your freshly swept cargobay. Try to get a few creatures/plants of each brand.
The easiest way to do this is to sample the entire ecosphere of a single planet. Simply get one creature/plant of each kind in the right order by carefully targeting with your beam, and dropping out what went aboard to early, so they will occupy a slot in the right position of your ships cargo. And once you have all slots prearranged, keep circling the planet and beam up everything. All creatures and plants will automatically be inserted into the right box.
After that, try to pinpoint rare creatures, like elusive herbivores or hard to find small plants with your ships radar by highlighting the needed species' dot in the terraform display of your radar, and go hunting. While you are at it, keep beaming up everything else. Sometimes you will have to wait a while for the species to appear, it might take ~1min sometimes.
You can invite your best friends on that trip, offer free spice samples and do loops in the planets athmospheres to celebrate the occaision. Don't forget the confetti.
After that, you'll be the proud owner of a full eco-set, ready to terraform anything bigger than a humpback whale. The trick mentioned by Random240 is really great too: Get your ship as close to the ground as possible, and teleport everything you put down back on board again. A splitsecond of ground contact is enough to populate the planet. If you run low on some plant or creature (sometimes the dropping goes all wrong), terraform a planet for only one level, using only your rarest plants and creatures, and go on a "I beam up everything and the kitchensink"- rampage again. Use the radar again if needed.
I did it and the work is really worth it.