I am not proficient in Inkscape and typically create things, most likely, in the most difficult way. I have created this logo by using the pen tool and bending the lines. I came up with this logo, which is great for a black and white variant of this, but I would like to make different iterations using color. The problem I am facing is that nothing is really connected and adding color, just completely warps everything. Is there a way to just connect everything into one shape and allow me to fill in the white with different colors? If this does not make sense, please let me know!

Maybe the paint bucket tool would help ???

So I tried that, but the fill does not fill all the way. It looks like the image attached. It is a great start, but it is almost like the paint bucket is filling the lines I created before I bent them. When I increase the stroke size, it overlaps the outline. I did not do a great job of separating my layers, so moving the outline to the top layer could be a solution, but it would be tedious.

Bucket fill has options like "Grow/Shrink" and works zoom dependent; the larger on screen the more precise the outcome will be. Then put the "fillings" under the black stroke work. Another but more elaborate option is to convert the strokes to black color filled shapes then Path->Union everything - then Path->Break Apart - now you have the black shape and all others separate to fill to your liking - not a one click bliss.

@Polygon

"Another but more elaborate option is to convert the strokes to black color filled shapes then Path->Union everything - then Path->Break Apart - now you have the black shape and all others separate to fill to your liking "

I'll have to try that technique. 

On the paint bucket fill idea, might be a good idea to create a new layer for it. 

 

@CelticOneD Not so easy because of the applied path effects but doable:

Poly - yeah I noticed - Inkscape crashed for me several times trying to union and break apart. I rarely get crashes. lol
Didn't realize it had taper stroke path effects.
The right wing is almost like the left wing but with several misc objects. Deleted the left and just cloned the right wing. That's when I realized it had taper strokes.  
So , I just went back to the paint bucket fill with layers for each color.  

As I said the Path effects are kinda showstopper here; they need 1. Path->Object to Path - then 2. delete stroke add fill - if you can find these it´s done in one go - and the wings with it´s filled open and overlapping strokes are the next hurdle I´d fixed - and of course just one half - then duplicate mirror and Path->Union.

I haven't poked into this document yet, but there is also the "Fill Between Many" Path effect that may work for some of this.

I cheated. Exported out as a png. Imported back in. Did a bitmap trace. Path Break Apart. Changed the colors. lol

32 Paths - surprised at that. 

With a copy, once all LPE are flattened and for the other paths strokes converted to path, I'd try to draw a wide rectangle bigger than design, select all and use shapebuilder tool.

Here is my attempt :

• I reorganized things (see objects panel) : grouped things, removed extra paths or ghost paths.
• I flattened paths with LPE, turned stroke to path for the regular ones, then I did path > union to unite theses differents shapes : the result is the path named oultine.
• On this path, I did an extensive node work to remove all excess nodes (I removed hundreds of nodes, I think) to shrink file size and smooth things : the less nodes, the smoother the design.
• Then I simply drew a rectangle bigger than outline, duplicated outline (and selected its duplicate and rectangle and did path > difference), then on the result I did path > break apart to separate all backgrounds.