With the atarimax flash-software.
That is what I do.
This makes a ATR (diskette) that you need to boot.
The booted software will erase/flash your cartridge.http://www.atarimax.com/flashcart/docum ... index.html
It's a command-line driven software package.
To create an ATR for a 1mb+IDE with bootrom (the 3.5F BIOS) here is an example:
D:\perl\bin\PERL MAXFLASH.PL -MYIDECART D:\MAXFLASHEXE\ -FLASHER
(Executed from the directory were I have the maxflash.pl file)
(Were I have PERL on D: and my XEX files in D:\MAXFLASHEXE\)
(You can replace the "came with the package" downloaded bootrom-file by the latest 4.6 bootrom-file)