It took me about a week to figure this out too, so I'll explain:
Download a Hex Editor like HxD (you can find the download here
http://mh-nexus.de/en/hxd/ ).
Open the start.dol in HxD.
Here's where it gets tricky, the first thing you gotta do is find the stage ID of the stage you want to replaced in HxD.
For example, let's say I want to replace Venom with Roy's Target Test stage... I'd find the location for Venom's Stage Select ID in HxD, and replace it's actual stage ID with Roy's Target Test Stage ID.
Here's a list of the ID's of most stages:
http://smashboards.com/attachments/sss-notes-4-txt.48676/
Venom's "Stage Select" ID is 3ED80C, so look for the row labeled 3ED800 in HxD (this might take you a while). You'll notice some numbers in that row that look like this "020D1216". The only numbers you need to worry about are the last two digits, 16, as that is the ACTUAL stage ID.
Now, you want to replace 16 with Roy's target test stage ID. This isn't included in the link I sent, but I managed to find the ID for this stage and a few others on my own (I'm not home rn but I'll send you what I've found ASAP). Roy's target test stage ID is 39, so your finished result should be 020D1239. After you've done that, save, and rebuild the ISO in GCR.
Now when you're back in Melee, picking Venom in stage select should take you to Roy's Target Test Stage.
Let me know if you have any problems.
EDIT: Here's are some of the other ID's (T meaning Target Test)
T Peach
?
______30
T GameWatch
?
______38
T Roy
?
______39
T Young Link
?
______17
T Bowser
?
______2A
T Ganon
?
______3A
T Young Link
?
______23