Ok, first off if your VBA is saying "batter has run dry" then you must insert a text format file in the same directory that your VBA is in:
Pokemon- Ruby Version
Pokemon- Emerald version
Secondly, if your gamboid application wont open your save file after your edited it on VBA and transfered it to your phone, thats simply because it changed the .sav file name. in which you must rename it like so "exact gametitle".sav without quoutes of course. Just copy game title, paste it as the sav file and there you go.