Troopers are great for getting through tough levels with characters you either don't have or don't have fully built up. But, there's something else to keep in mind. You get trooper badges for every trooper you bring along, so every round you play should have a trooper with you in some slot.
My general idea is this: farm levels that give me decent rewards (gold, evo materials, etc.) while also bringing along a trooper. I generally stick to a level I can beat with just an Eddie, bring along an Eddie that I'm leveling up, and bring along an ally. Once I have that basic team built, I'll click on the "Auto replay" and choose to replay with troopers. I'll let that run while I sleep many times, but only if I check my inventory first to make sure it hasn't filled up either on shards or talismans.
By playing all of your troopers each day (all 50 if your player level is maxed), you will find that everything in the trooper store becomes quite attainable. As an added bonus, the more you bring troopers along, the more likely troopers will bring along your character, awarding you additional trooper badges.
Do keep in mind that if you get a loss and don't continue, neither you nor your trooper will get those badges. It's fine to try passing new levels with strong troopers, but it's not advised to go marching blindly into battle when you don't feel your team has a chance. If you feel it's risky, we recommend playing that battle without a trooper.
A few terms that apply to this concept:
Back Seat / Shotgun: An Eddie coming along that is not being actively played
ShareAnEddie: A movement started in some of the Facebook groups and on the forums to encourage the sharing of Eddies, which make farming with troopers quicker and more reliable (as they can ride shotgun)