I think you are on the right track, running long running multi-parameter scripts directly from the commandline can be cumbersome and after a while you never know which command actually succeeded. A hint to make your life easier: make a simple shell script wrapper for the trinity call. That way, you also document the parameters used. A step you have to do before is some quality control to check if you need to trim your reads. I should maybe stress that running a QC process is the point to start from, not running the assembly outright. Run fastQC on your files first to see if the quality is high and whether there is adapter contamination.

Here is a simple command to start running Trinity from, without using trimming

#!/bin/sh
set -eu

TRINITYCMD=Trinity # adapt this if Trinity is not in your path
# you need to adapt max_memory and CPU to your server 
$TRINITYCMD   --seqType fq --max_memory 500G --left $1 --right $2 --CPU 60 --output Trinity-1 
# change the output directory each time you run something fundamental, like adding trimmomatic option

Save the script as run_trinity.sh, make it executable and run it as:

nohup ./run_trinity.sh file1.fq file2.fq &

That way, the script will not be interrupted when you log out. Debug output is in nohup.out.