I'm not sure I follow.  If you take an image with Acronis (in Windows), and have incrementals setup, it will only ever backup the changes that have occured between each backup.  You can achieve incremental backups using the offline bootable recovery media as well.  This is basically doing what you want, but all of it is happening in the background so that you don't have to follow what changes are being backed up

Now, for restores, if you wanted to pick and choose just certain files/folders that changed with the last incremental, that is harder to determine.  Ideally though, you could do a full restore with your incremental backup and it would have all of the changes as of the time the last backup was taken.

If you are more worried about being able to restore files/folders as of a certain period of time, you may want to consider setting up "Sync" instead and syncrhonize your files/folders to a specific location.  Acronis has this capability (I have not used it though).  Alternatively, there are other programs like "Alwaysync" that you may want to consider.  I'd give Acronis Sync a try first though. 

Synchronizing data

After booting from my portable HDD into Acronis, I have to select Backup > My Data where I have to choose the files I want to backup.  My concern is that I may miss some of the folders as I haven't got them listed elsewhere so they may not get backed up.  It is only then I get to choose where, in my case, an existing archive.

The problem as I see it is that everytime I boot using the HDD, I have to select my folders, I have to tell it that I want to add it to existing archive and where it's located and then I have to tell it to do it in which mode.  The number of folders could be many and it is not always easy to remember which folders to backup on which PC.  By the time you've finished racking your brain trying to remember whether you have everything covered and you've hit the proceed button only to realise you've missed the mode option....

If I am going to have to try and remember which folders I want to backup, the chances are some will be missed.  I was wondering whether there was a way of opening a settings file which says something along the lines of 'back up folders X, Y and Z' to 'ABC location' in 'incremental mode' so that it is the same every time.

Ufortunately, not to my knowledge.  The default bootable media is static in the sense that every time you boot it, it is exactly the same as the way it was originally created ... nothing gets saved in the bootable media so I don't see a way that the applicaiton, if it were possible, would even be able to implment such a settings file.  This is a limitation of both the Linux default bootable Acronis media as well as the WinPE bootable media, since WinPE, by Microsoft desigin, is also built this way so that users wouldn't be tempted to create WinPE and attempt to use it as their primary Operating System without a Microsoft license. 

I'm curious, but why not just make incrementals of the full system in the first place?  That will still give you the changes that you're looking for without having to go into specific directories each time.  The only downside is a little overhead with changes to the OS and applications, but the incremental changes for those would be pretty minimal.  If backup disk size is an issue, you'd probably save more time and money in the long run upgrading to a bigger backup drive to support this than manually tweaking incrementals with each offline bootable recovery backup.

Alternatively, in your case, you might be better off creating your backup in the full Windows version of ATIH and running the backups from within Windows as this is customizeable and could/would be saved in a backup plan.  Then, use your offline bootable recovery media to take supplemental full backups (or incrementals as you have been or as suggested above) every now and then as a secondary backup job for "just in case" redundancy.  

As another possibility, and I don't know if this would work in your situation, try to create a single main location where your changing data would be taking place (for instance a single folder on the root of your C: drive titled "data".).  Then create other folders within that one where the data you are concerned with would be directed to, instead of the current places they are getting written to when Windows is running.  You could then boot your bootable offline recovery hard drive and run incrementals on just that main "data" folder and the process would not be as in depth as what you're having to currently do.  

On the whole, I do try and keep data in one place, however sometimes data is written elsewhere and not on all machines so you have to remember which machine to backup which files/folders.  Other users don't always put the data in one place either so you have to second guess where people save things too!!

I was beginning to wonder whether an incremental backup of the disk was the way to go and you've just confirmed it is an option.....

Thanks for your assistance.