We don't recommend inserting CodeReplace macros automatically for the following reasons:
1) The automatic macro could be in a critical code in your application which will decrease the performance of your application. Notice that the CodeReplace code will be run as emulated, which runs slower than the original code
2) The automatic macro protects an area of your application which you are not interested to protect
3) It can contain a macro restriction, please, refer to:
We recommend you inserting CodeReplace macros in your source code directly (using the CODEREPLACE_START - CODEREPLACE_END markers), so you have control of where the macros are placed and you can make sure that your sensitive code (serial checks, trial/registration checks, etc) are protected. Also, you make sure that you avoid the CodeReplace macro restrictions at http://www.oreans-support.com/kmp/index.php?/article/AA-00272
In the Examples folder in Themida, you have examples in several programming languages about how to insert macros in your source code.