11:24 a.m. on June 24, 2012 (EDT)
smithcreek,
This is actually a very good question and the fact that you ask it tells me you are further along in skill than you may think.
These are things you don't question until you begin to do real navigation off a trail system.
I too venture into some very dense swamps with meandering creeks and rivers that I must navigate around, no trail system.

Looks kinda like this is the flooded areas, very limited visibility & no distinguishable terrain features in view.

Looks like this on high ground, again no distinguishable terrain features in view. This is the view in winter, in summer you can't see this far.
The water levels and water locations can change with the seasons. Right now we are in the wet season here in coastal SC.
Anyway, I do understand exactly what you are dealing with.
I can only tell you what I have been doing and I am still in a learning curve myself.
Here is my approach:
I only use full size USGS topos in 24:000 scale (7.5 minute topo). The level of detail you get with a larger map plus being able to study the surrounding areas gives me a better understanding of the lay of the land. I don't like small maps centered on my location and printed out on my printer for this application. I need to see and understand the bigger picture.
I take the time to draw a full UTM grid on the map using the tick marks in the margins. You can use Lat / Lon if you wish, I just prefer the UTM since it is easier to count & measure in multiples of 10, (10 meter, 100 meters, 1000 meters) especially if I am counting paces or amount of time walked.
I take the time to really study the map before heading out, noting any roads, towers, boundaries, creeks, or subtle elevation changes.
Once in the area I keep the folded map in a clear map case with a pencil, map ruler, and UTM grid tool hanging from my pack on a short lanyard. I note the elevation & location I'm starting at, as well as the types of plants growing in that area.
I mark my starting location on the map, decide on a course, and let the map hang back at my side to free up my hands for compass work. Next I take a bearing with the compass and get ready to begin hiking in that direction.
If I am hiking to a creek or well defined swampy area on the map I don't bother counting distance but rather use the water as a backstop, when I get there I know where I am on the map using my starting point & compass bearing.
If not walking towards a distinguishable area, I can either count paces or use a stop watch to measure my distance walked. I already know how far I can walk in a minute, or five minutes within reason and many times I use this method instead of counting paces so I can free up my mind to pay attention to other things. I let a stop watch keep up.
With either method I keep up with, and mark my location on the map, as I progress. I keep a log of compass bearings for each turn on a 3 x 5 card in my map case. I also pay very close attention to what types of plants are growing in each area as I walk. If you can familiarize yourself with the plants & trees that grow on dryer soil as opposed to wetter soil you can use this to help you navigate towards or away from water - or high ground. I have found this to be very helpful in areas with quickly changing features (wet & dry areas) as is typical in bottom land hardwood swamps.
I try to pay attention to the water as well, is it flowing? It it still? Look at the map and see what sections of water are free flowing (and what direction) into larger bodies of water as is typical in watershed centers where I usually find creeks and rivers - as opposed to still water or ponds (boggy areas) often found trapped in sub drainage basins (look for depressions on the map that are surrounded by high ground).
In other words the terrain features & elevation changes in flat swampy areas are much more subtle than in the mountains, but they are there. I try to use all the visual clues I can to tell me where I am on the map, as well as what direction I should head. I try to plot out a course that takes me close to any distinguishing features I can see on the map - creeks, high points, open areas, etc.
Pay attention to plant type as this is key to knowing if you are approaching low wet areas or higher drier areas. Where I like to hike Canes, Ferns, and Dwarf Palmetto all grow in different areas. I ask myself do I see mostly Lob-lolly Pine or Cypress trees where I'm at? This is handy for finding your way back out so make a note of it.
Study the entire area before heading out so you understand how that particular watershed works, which way the water flows and where. Know where the boggy areas are and where the higher areas are.
Try to find and use backstops on the map if at all possible, these can be long linear terrain features like creeks, edges of large flooded areas, unique stands timber, or open meadows / marshes that you will approach at a 90 degree angle, or Tee into. You can also use these same features as a handrail by navigating parallel to them.
I do my best to keep up with these things:
Starting location.
Compass bearing.
Distance covered (counting paces or time elapsed).
Keep up with where I should be on the map & record bearings on a piece of paper (for backtracking).
Pay attention to what I'm seeing, keep notes on it and try to reconcile that with the map.
Try to plot a course on the map that carries me towards, or close to, distinguishable terrain features so I can use backstops & handrails.
Remember that not all tributaries will be marked on the map, or may be gone in drier times.
Know where the closest roads are in the area in case I need to bail in that direction.
If all else fails (and it frequently does) I pull my coords from my GPSR, mark my correct location on the map and start over again from that location with map & compass work. I use the GPSR as a learning tool to determine what mistakes I have made or how far off I am.
I am learning that some of this is an art, you just have to get out there and do it. The finer points are not something you can learn on a trail system or from a book.
I hope I didn't confuse you too much, and I'm sure I left something out that I may add in another post.
Mike G.