You didn't say whether the compiled FLAC is exe or dll and you did not specify what version of CUERipper.
I'll assume exe and CUERipper 2.1.9
An easier approach has been requested.
https://hydrogenaud.io/index.php?topic=118915.0#post_CUERipper
Start by adding the encoder to CUETools and testing it.

The settings shown assume you copied the exe to the CUETools main folder. Alternately you could add the path to the file (e.g. C:\flac\flac.exe) or add the location to the %path% in the Windows Environment Variables.
Make sure you adjust the slider to a compression setting before testing or you'll receive an error message.
Exit CUETools
Next open the CUETools settings.txt file (in %APPDATA%\CUE Tools or if running as portable you'll find it in the \CUE Tools subfolder)
Find your new encoder
Advanced={
= "encoders": [
[...]
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "qaac.exe (tvbr)",
= "Extension": "m4a",
= "SupportedModes": "10 20 30 40 50 60 70 80 90 100 110 127",
= "EncoderMode": "80",
= "Path": "qaac.exe",
= "Parameters": "-s -V %M -q 2 - -o %O"
= },
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "my flac",
= "Extension": "flac",
= "Lossless": true,
= "SupportedModes": "0 1 2 3 4 5 6 7 8",
= "Path": "flac.exe",
= "Parameters": "-%M - -o %O"
= }
= ],
= "decoders":
copy the text including the comma after the closing curly bracket from the previous encoder settings
,
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "my flac",
= "Extension": "flac",
= "Lossless": true,
= "SupportedModes": "0 1 2 3 4 5 6 7 8",
= "Path": "flac.exe",
= "Parameters": "-%M - -o %O"
= }
(you should probably save a copy of the CUERipper settings.txt file before this step)
open the CUERipper settings.txt file (in %APPDATA%\CUERipper or if running as portable you'll find it in the \CUERipper subfolder)
Find the last encoder
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "qaac.exe (tvbr)",
= "Extension": "m4a",
= "SupportedModes": "10 20 30 40 50 60 70 80 90 100 110 127",
= "EncoderMode": "80",
= "Path": "qaac.exe",
= "Parameters": "-s -V %M -q 2 - -o %O"
= }
= ],
= "decoders": [
paste the text you copied after the closing curly bracket of the last encoder (including that comma)
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "qaac.exe (tvbr)",
= "Extension": "m4a",
= "SupportedModes": "10 20 30 40 50 60 70 80 90 100 110 127",
= "EncoderMode": "80",
= "Path": "qaac.exe",
= "Parameters": "-s -V %M -q 2 - -o %O"
= },
= {
= "$type": "CUETools.Codecs.CommandLine.EncoderSettings, CUETools.Codecs",
= "Name": "my flac",
= "Extension": "flac",
= "Lossless": true,
= "SupportedModes": "0 1 2 3 4 5 6 7 8",
= "Path": "flac.exe",
= "Parameters": "-%M - -o %O"
= }
= ],
= "decoders": [
Save the settings.txt file for CUERipper
Open CUERipper and test the encoder.