I made 2 paths, then take one on the each other, grouped and then used extrude and bevel fx. How you can see, in place where they're overlapping you can see the countours of the top path. How can i fix that problem? Is there any way to mix these paths or to fix it i'll have to manually redone the paths to make one?
Don't group. Apply the 3D effect to each path individually.
By grouping you tell the 3D effect to treat everything as 1 object. The remnant of the top contour is only there due to slight lighting hitting it, otherwise it wouldn't be visible at all.
In short, if you want it to appear as 2 objects, use 2 objects not 1 group.