You could always open the RSBE01.gct file with GCTEdit, then delete the Disable Custom Stages code so that your PM Build will load your custom stages.
Here are some specific step by step instructions (please note that these instructions are for homebrew users):
1.) First, make a back up of your RSBE01.gct file (located in the "codes" folder in the root of your SD Card or USB thingy), just in case something goes wrong. Once you've made your copy, download GCTEdit. You can download it here
https://www.dropbox.com/sh/kquyhpig2xuda3z/ggm1b8tmF5
2.) Unzip GCTEdit, then open the GCTEdit program when you are done extracting the files. Once the GCTEdit program starts up, click on "Open GCT" in GCTEdit, which is located near upper right corner of the window.
3.) Now search for the RSBE01.gct file that is in the "codes" folder, located in the root of your SD/USB device. Click on it, and wait for GCTEdit to open the gct file.
4.) Once GCTEdit opens the gct file, click on "Save TXT".
Save it as this:
example.txt
5.) Now open the text file you just created from GCTEdit. Now press both"CTRL" and "F". A text box will appear. Now copy and paste this code into the text box:
This is the code that disables custom stages. Click on "Find Next" in the text box, and it should highlight the code for you. Once highlighted, delete the code. Be sure to close any gaps in the code list upon deleting the Disable Custom Stages code.
6.) Now save the text file. Not "Save As", just "Save".
7.) Use GCTEdit to open the text file you've just edited. Click on "Open TXT" in GCTEdit to do so, and search for the edited text file.
8.) Once GCTEdit finishes loading the text file, click on "Save GCT".
Now save it as this:
RSBE01.gct
9.) Replace the RSBE01.gct file in your codes folder with the RSBE01.gct file you've created.
10.) Eject your SD/USB device safely, then insert it in your Wii. Start up your build of Project M. If you did the above steps correctly, then you should be able to select your custom stages in the stage select screen.
A word of warning:
If you save your custom stages on your SD card, then edit them, there is the possibility they may freeze your game. The safest way to play them is to save your custom stages on your Wii. That way, when you edit them, they won't freeze randomly during editing, upon selection, or after a match ends. I hope this helps.
Also, the stage select screen will look a little wonky when you go to the custom stages page. Do not worry, it will function as normal. However, if you have a lot of custom stages, the page buttons will be obstructed by the custom stage list. This is easily resolved by simply pressing the L or R button (you can scroll through the stage pages with them).
I hope this helps!