Two installation, one webspace, root&subfolder

Hey there, I got a problem to gettin two installations run. Both with permalinks. The first in the root and the second in a subfolder. The problem is when I configure the installation in the subfolder it always overrides the .htaccess in the root (I already put it on 644 and 444). And I already used the search but most of the answers say put it on 644 and it does work – but it doesnt. Any ideas?

Thx