Yes, this will cause loss of resolution. For labeling use a drawing program; I use inkscape, which is a free program, but there are plenty of alternatives, such as Adobe illustrator ($$$$$), even Powerpoint will work better than Word (save as then change pptx/ppt to png or pdf). For combining images (e.g. overlaying different color images) you need to use an image processing program such as Photoshop ($$$$), however, imagej (free and designed for this sort of thing - have a look at its variant FIJI for pre-packaged immuno applications), and GIMP (also free) work equally well.
To avoid loss of resolution in the labels it is best to save them in a loss-less format such as png or pdf. JPG/JPEG images are useful for pictures only, and even then if you can, save original images as TIF format, then export to jpg for presentations and the like. TIF images retain all the pixel data for each pixel (so you use these for data analysis), whereas JPG groups pixels of the same type and says that these are one pixel, so you lose data.