Yes. You can do this as long as you can put the extensions in different groups.
I only know how to do this the asterisk way. If you need it done the Trixbox way, you'll need to wait for a Trixbox expert.
Let's say you have 6 extensions: 101, 102, 103, 104, 105, and 106. Let's also say that you want 101-103 to dial out using trunk A, and 104-106 to dial out using trunk B. The answer is to put them each in their own contexts:
Thus, your extensions.conf will look something like this:
[use-trunk-a]
exten => _NXXNXXXXXX,1,Dial(${TRUNKA}/${EXTEN})
[use-trunk-b]
exten => _NXXNXXXXXX,1,Dial(${TRUNKB}/${EXTEN})
Your sip.conf will look something like this:
[101]
type=friend
context=use-trunk-a
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no
[102]
type=friend
context=use-trunk-a
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no
[103]
type=friend
context=use-trunk-a
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no
[104]
type=friend
context=use-trunk-b
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no
[105]
type=friend
context=use-trunk-b
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no
[106]
type=friend
context=use-trunk-b
secret=blahpoly
host=dynamic
dtmfmode=rfc2833
username=polly
disallow=all
allow=ulaw
progressinband=no