> Do you mean I should use 3dLMEr with the trial-level estimates?
Are you interested in the population-level covariate effect across trials? If yes, you can use 3dLMEr (or 3dLME) as I previously suggested.
> Can I add covariates at subject level when doing 3dDeconvolve in this case?
If you're not interested in the population-level covariate effect across trials, you have two options: 1) the same model with 3dLMEr (or 3dLME), or 2) you could model the covariate effect at the subject level, and the proceed with the condition-level effects as input for your population-level analysis with 3dMVM.
Gang