It depends on the situation.
The first mission in either 688i or SC (??) had you depart from Groton and sail south to deep water while avoiding surface ships. The intro to that mission was sneaky, but it advised you stay close to the bottom (like 20 feet above) so you could arrive at the proper point on time.
So, it depends on your situation and what the bottom is like (pre-RA). It also depends on depth and your mission tasking. Besides layers, the bottom type could be rocky (smooth), sandy, or muddy. Check the mission description and briefing for clues on the bottom type or take a quick peek at the mission in the editor to find out what you're dealing with.
You can also use sea state to your advantage (pre-RA). Rough seas can make detection tougher but also carries the risk of broaching.
In both cases, what helps hide you can also make it tougher to track the enemy. So plan wisely.
Figure out who's trying to find you. If you have four contacts you're tracking, take the time to position yourself so you can identify them. If it turns out you're tracking two ASW platforms, a torpedo retriever, and a fishing boat- that gives you a lot of information to exploit.