I customised amember 4 on few things to support my membership website. Would I experience any problems when upgrading to new version such as 4.2 beta, if so what would it affect.
Yes there will be issues if you've changed aMember files. To avoid such issues add your customizations to the files that is not included in aMember PRO installation package. For example here is how you can customize aMember look so it will not be overwrited by upgrade: http://www.amember.com/docs/Themes_and_Templates php code can be placed to a plugin or module, or into /amember/default/configs/site.php