No you will not loose troops if you go in minus grain.
Raids -->>are pretty good provider of your much needed resources, you need to be active and use all possible raids and amount or resources you can raid from a city-->>for that good idea will be to upgrade Port and Harbor so you can fully benefit from the amount of resources your units can carry at one time.
To avoid Loosing resources being an active player is a must, this is the most easier way to avoid being farmed by others
Acropolis -->> upgrading fully will allow you to build army and also sent them automatically to your Acropolis once they been trained.
But to address this issue is a good idea to also tackle few things such as upgrading :
Farms -->>> upgrading fully to increase production of grainAcademy --->>use scrolls to upgraded Grain consumption reduced by -8% (more units more reduction)
Eleusis -->>Signing agreements for it will allow you to build Temple of Demeter
Temple of Demeter-->> when fully upgraded has a bonus of consumption of grain reduction by 89%+ additional fallen units can be revived at the healer
Dominion -->>at level 15 gives 15 % grain production boost
Resource Production +25% -->>available for 1 day and 3 days (Grain tab in the Market)
Temple of Xenia-->> Increase your resource production
I hope this help, Good luck !