Hi Yorgos,
Maybe you can leave the combining to the application? Just typing "e with dot above", then "macron" could do the trick (U+0305 COMBINING OVERLINE, not the spacing one ¯ you have in the layout on the , key now). ė + U+0305: ė̅
Another approach is to assign a sequence of two Unicode characters to one key, which can be done with Ukelele.
I encourage you to read Ukelele's tutorial :) also because, apart from the above, you may want to create dead keys for the diacritics, to make your keyboard layout less crowded and easier to remember.
As an inspiration, you can activate the layout "U.S. Extended" and see how it works. (However, with that layout one can't type "e with dot and overline", as far as I can see.)
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