It is recommended that you edit clips in the timeline prior to creating Batch FX. If you perform operations such as trimming a clip or adding a timewarp after completing an effect, you risk affecting the timing of the effect or trimming out frames that were intended to be part of an effect. Also, by getting the edit as close to final as possible before doing effects, you avoid spending too much time rendering.
The following are suggested workflows for using the Batch timeline. Regardless of which workflow you use, you have the option of saving modified clips to the Desktop or to the _Edited library. See Managing Clips in Batch.