Hi,
I main on my sniper, I hope my advice can help.
For any spec don't engage when they have entrench up.
MM snipers should be the easiest to kill, as people said LOS them and wait for the to leave cover.
For lethality make sure to interrupt their cull.
I wouldn't engage an engi at all. Whenever I play engi I tend to do well against juggs. They open with a slow then stun followed by ep and SoS will wreck you (usually the majority of the damage will be done while your stunned in their plasma probe).
Save cooldowns for ambush, SoS, and cull- except for an engi pop cds when they put the shock probe on you.
Also don't stand in their orbital strikes, that's a guaranteed lose for you, just disengage if you can.