Is it better to use these on one Trans Entropy at a time or just let all 4 upgrade randomly?

If you have extra credits to spare, then yeah, if not I would suggest to make it all random out of the 4.

Ideally, a 10 and a 5 is best. This is for two reasons:
if your ship is on the small side, using just the 10 or 10+5 will give awesome def/deck ratio
if new defense tier come out, you can just keep the 10+5(or if multiple tiers come out, just the 10) so you get max defense benefit. This is rather unlikely but better safe than sorry.

However, if the shuffling is too expensive for you AND you have a large enough ship that you will probably keep all 4 module on most of the time, use them randomly is fine. #2 is very unlikely so not really worth waiting for. But if you can afford it, go safe.