Yes, you can use the compiler options to define your flags as:
<system.codedom>
<compilers>
<compiler language="c#;cs;csharp" extension=".cs"
compilerOptions="/D:FirstDefine,SecondDefine"
type="Microsoft.CSharp.CSharpCodeProvider, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" warningLevel="4">
<providerOption name="CompilerVersion" value="v4.0" />
<providerOption name="WarnAsError" value="false" />
</compiler>
</compilers>
</system.codedom>
Then on your code you can use
#if FirstDefine
// ... your code
#endif
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