This image shows the spectrum of the clipped audio (red) vs. the spectrum of the audio after declipping (yellow/orange), the difference is about 20 dB. It's pretty clear from this image that the declipped audio is much easier to encode.
As a side note: This means that to improve your codec's response you should always use the declipper for streams, HD and DAB+ stations!
So now what?
If you feed your processor that contains the Declipper with a lossless source, without making any changes to the audio, you're fine. If your music library consists of something like MP3's, you're doomed - go away and start re-ripping everything. (Sorry, I can't make it much nicer than that).
In other situations, try to declip before you do anything else. This is definitely not the easiest solution, and live material still might arrive with clipping which wouldn't be fixed properly. Anyway, there are multiple ways of doing this.
You could for example declip all the files when you put them in your music library. Please keep in mind that future repair filters, declipper improvements or even declipper settings changes might force you to do this again, so at the very least, keep your originals as well. Also make sure that you store them in a high enough bit depth, and under no circumstances use a lossy codec to store them.
Another option is to run part of the processor that contains the declipper before the steps that cause the changes to the audio, and the rest afterwards. In case of Stereo Tool, you can run 2 copies, in case of several of the Omnia products you could use patch points to get the declipped audio out, and send it back in after performing the pre-processing.
A few final notes
It probably doesn't hurt to declip twice (but it might if you change the audio in between). So, there are situations where you might want to perform the declipping on each file, but still enable it on the processor as well.
If you store the output of the declipper in a file with the same bit depth as the original, due to the extra headroom required you will introduce some hiss or quantization noise. For 24 bit files that's no problem, for 16 bit files it might be, especially if you use processing that can boost the level a lot. If you use Stereo Tool you could use the Dequantizer to increase the bit depth back from 16 to about 18 or 19 bits, but not going back and forth is always better. So it's better to store the resulting files in a higher bit depth.