About GBA saves and VBA, File -> Import -> Battery File
And N64 with PJ64, use the N-Raghe input plugin: "Options" -> "Settings" -> "Input (Controller) Plugin" -> select "N-Rage..".
Then menu "Options" -> "Configure controller plugin" -> "Controller pak" tab -> change "none" to MemPak" on the combo box -> "NewMempak/Browse" -> browse to your .n64 save file