There will be projection issues. It's just the nature of world maps, all the various options will have huge issues. As they get closer to the poles equirectangluar gets nearly impossible to work with. If you are using photoshop I heard it has a utility that allows you to work on a 3d sphere that you can then unwrap. I don't know if GIMP also does. Indeed because of the difficulty of working on a equirectangular (or any flat world map) I'd recommend planning it out on a 3d sphere and then unwrapping it, if you have that option (If not photoshop and you are familiar with Blender or another 3D program this would be fairly simple, but if you have to learn how to use the program from scratch I don't think its' worthwhile (unless you also want to do that for some other purpose)). If not then just go for it anyways with GIMP or Krita, you can always fix things later when and if you have to.

I'm also pretty sure G Projector will allow you to convert a equirectanglur map and then scroll around the world and you can then take a piece out in a more favourable projection. It will also show you how screwed up your landforms might be if working from scratch on an equirectangluar map, and then you can figure out how to try and fix them.