Problems with R/RAqua

I work now for quite a while with the R Darwin/X11 version from Fink  
which works fine.
Today, I downloaded and installed RAqua from CRAN, which I can start up  
directly from the Applications/ folder. I also changed the links as  
recommended on the R developer page. However, when I try to start RAqua  
from X11, I get the following message:

christof% R
dyld: /usr/local/lib/R/bin/R.bin malformed library:  
/usr/local/lib/R/bin/Help (n
ot a Mach-O file, bad magic number)
Trace/BPT trap

Any suggestions to what happened here?

Apparently, there are different paths in the terminal and X11:

Terminal:
christof% echo $PATH
/sw/bin:/sw/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/ 
X11R6/bin

X11:
christof% echo $PATH
$PATH:/usr/bin:/usr/sbin:/usr/local/bin:/sw/bin:/sw/sbin:~/bin:~/sbin: 
~/usr/bin:~/usr/sbin:~/usr/local/bin:~/usr/local/sbin   
/usr/local/sbin:/usr/X11R6/bin:/bin:/sbin/:/usr/X11R6/bin

In the first case, the R version (v1.7) from Fink is searched for, in  
the second case the newly installed RAqua version (v1.8).

My questions:
How and where can I permanently change the path for both the Terminal  
and X11?
Can I still use RAqua within Xemacs that I installed from Fink?

Thanks for your help!
Christof