Hi Bart,

As you can probably imagine, I don't use my R-8 on a daily basis nowadays (to put it mildly), so I've had to try this for myself to get an idea of the problem you're describing.
Here's what I found:

When the R-8 is not playing a pattern, the R-8 immediately accepts any change I make in R-8 Manager's "Instrument" or "Pads" window. That is: if I then play the instrument manually by pressing the corresponding pad on the R-8, the sound is different.
However, when the R-8 is playing a pattern, the R-8 ignores any change I make in the Instrument or Pads window.
So if I understand your question correctly, I'm afraid the answer is no.
(Maybe it was simply too difficult for the R-8 (a device from 1988!) to change the sound parameters during pattern play?)

I think that all this is in line with the "Pattern Writing (Advanced)" section in the R-8's Owner's Manual (which is (or at least used to be) available as R-8_OM.PDF from Roland's website, if you haven't got a paper copy yourself).
As the flowchart for Song and Pattern Play (on p. 77 of the manual) indicates, during song and pattern play the Sequence Parameters (which you have programmed into the pattern) plus the Sound Parameters determine the output.
The Performance parameters have no effect on Song/Pattern play (p. 78):

- Value of a Performance parameter is effective only on the sound played by the relevant key pad. It has no effect when rhythm patterns or a song is being played.

- The set Performance parameters are entered into a rhythm pattern in the Pattern Writing as Sequence parameters (sound data).

Your other question:

When the R8-manager is running, I have double sounds when playing a pattern ? When I quit the application it goes back to normal...

The only explanation I can think of is that you have an undesired loop in your MIDI setup.
During pattern play the R-8 outputs a MIDI message whenever an instrument is being played, and apparently in your setup with R-8 Manager these messages get fed back to your R-8, leading to the double sounds.
In R-8 Manager you can monitor any incoming messages: open the "MIDI input messages" window from the main window via View -> MIDI -> Input messages, then press the Record button.
You should ensure that R-8 Manager doesn't loop these messages back to the R-8:
In the "MIDI devices" dialog box (opened from the main window via Options -> MIDI devices), ensure that the R-8's MIDI input device doesn't state the R-8's MIDI output device as "Thru output device".

Hope this helps,
   Mark.