Every time after installing a custom ROM over a different ROM you will lose the contents stored on your smartphone's system partition. This post contains info on how you can use a root-based application like Titanium Backup to backup data from installed applications in order to restore it after flashing a new custom ROM.
Titanium Backup is a tool created by Titanium Track and it is one of the most popular Android apps with over 50 million installs only from the Google Play Store data. Note that by using this application you will first need to root your smartphone. This tool is not supported by stock Android firmware, which is why you won't be able to use if you're currently running such ROMs. Use Titanium Backup for free with limited functionality or choose to upgrade to PRO version and get your hands on one of the best backup applications for Android.
The Titanium Backup *ROOT tool can be used to backup and restore, freeze apps Data and Play Store links (PRO features). All of these are supported for system applications, protected apps, external data stored on the SD card. Use this tool to move to and from SD card apps and apps data. Other features that you will after upgrading to PRO features are as following: 0-click batch restores, create multiple backups per single application, use it to backup and restore SMS, MMS, Calls, Bookmarks, Wi-Fi AP as XML data; multi-user app data, apps freezer, convert user apps to and from system system apps, integrate system apps updates into ROM, Market Doctor, Destroy all market Links function, hypershell speed, backup apps without the need of closing them, create you own version of update.zip that can keep apps and data, restore individual applications + data from non-rooted ADB backups, restore individual applications and data from both CWM and TWRP backups, dalvik cache cleaner, unlimited schedules, change Android ID, restore it from backup and factory reset, protect backup against deletion, send backup to cloud and multiple others.
Applications and data can be synced to cloud storage services using Titanium Backup, which means that you won't forget where you saved these types of files. You can use Titanium Backup to sync to and from Dropbox, Box and Google Drive. Choose whether you want to manually sync apps or create a schedule. Also, you can use the TB Web Server to download and upload backups as single zip file on your PC.
Download Titanium Backup *ROOT free from this Google Play Store link here.
Download Titanium Backup PRO version from Google Play Store link here.
After you install this app on your device, launch it and then use its functions and features in order to backup installed apps + data. If you have problems using this application then you can ask for more help in comments or check the developer's web page here.