The new QNAP firmware (3.4.0) supports 802.1q VLAN tagging, but you can't create multiple interfaces in different VLANs on the same physical interface through the webinterface.
In the case of link aggregation (LACP 802.3ad for example), that means only 1 VLAN and 1 IP address can be used.
Fortunately, QNAP allows full access to the underlying Linux system. Adding a VLAN interface goes like this (the example uses VLAN 234)
# /usr/local/bin/vconfig add bond0 234
# ifconfig bond0.234 192.168.2.30 broadcast 192.168.2.255 netmask 255.255.255.0
of course, this change is not permanent, a reboot will not automatically start this interface. I'll blog about making it permanent later.