It all comes down to your network as to how you should setup VLANs. You don't need them unless you are trying to segregate various wireless or wired devices from other devices.
Now my setup a going to be different from most as I am not using the R9000 as a router, but just a wifi access point. Also important is that my R9000 is connected via the SPF+ port, and not a standard RJ45 to my core network (VLANs work fine on this interface, but the others are much more complicated). My core network switch does all the inter-VLAN routing (that I allow), and my edge router does the routing to the internet. I setup two additional VAPs (virtual access points) on each of the 2.4 and 5GHz bands. This is done in DD-WRT under the wireless page, by clicking on the "Add" button under "Virtual Interface" after each of the radios (there are several tutorials/how-to's on this for how to create a guest network under DD-WRT, make sure you check the "AP Isolation" option on them). Once you have the virtual interfaces, you can create the additional VLANs by going under the "Setup"->"Networking" tab and adding the VLAN tagging to eth0 (which is the SFP+ port). You can use any VLAN ID you want/need, except for 1 or 2 as they are already in use by the router and can cause problems if you do not already understand that they are in use and what they are being used to do. You will now need to create new bridge devices for each of the groupings of devices you want to have (in my case, I have 2 additional bridges, one for a "guest" network, and one for "internet of things" devices) under "Bridging" section on the same page. Under the "Current Bridging Table", you want to make sure you remove the new VAP interfaces, the additional eth0.<vlan id> devices, and additional bridges from the "br0" bridge (otherwise they are all just one network). Save the settings, and reboot the router (at this point, you have not done anything that will cause problems).
After it reboots, you need to go back to the "Wireless" tab and configure the new VAPs that you created (if you didn't do that already), basically you are just setting a new SSID and encryption keys (it will use the same bands and other physical network settings as the original device). Now under the "Setup"->"Network" tab, you can configure the eth0.<vlan id> interface, giving them an IP address and netmask (defining the network for the VLAN). These need to be different from each other, otherwise it will not be able to route them correctly. I suggest simply using the VLAN ID as the third octet in the subnet (so 192.168.<VLAN ID>) and if the R9000 is going to be your router, I suggest making the IP of the eth0.<vlan id> be 192.168.<VLAN ID>.1 (if it is not going to be the router, you can make it .2 or .254).
Now comes the tricky part, assigning the VAPs and eth0.<vlan id> to the new bridges that you created. This is where I had to use a startup script under "Administration"->"Commands". ABSOLUTELY DO NOT SIMPLY PUT AND SAVE THE STARTUP SCRIPT UNDER HERE THE FIRST TIME! You need to test it, preferably via a "ssh" connection to the router and running the commands directly there and verifying first.
As a startup script I have the following:
vconfig add eth0 8
ifconfig eth0.8 up
ifconfig eth0.8 txqueuelen 1000
brctl addif br1 eth0.8
brctl addif br1 ath0.1
brctl addif br1 ath1.1
vconfig add eth0 10
ifconfig eth0.10 up
ifconfig eth0.10 txqueuelen 1000
brctl addif br2 eth0.10
brctl addif br2 ath0.2
brctl addif br2 ath1.2
I used VLAN ID 8 and VLAN ID 10 as my "guest" and "IoT" VLANs. The above sets up the appropriate VAP devices and VLAN tagged eth0 devices into bridge device br1 and br2 respectively. If you are only setting up one VLAN, you don't need the lines that repeat. The "vconfig add eth0 8" is adding the VLAN ID 8 to eth0 correctly. The next line "ifconfig eth0.8 up" brings the new tagged interface device online. "Ifconfig eth0.8 txqueuelen 1000" sets a transmit queue length of 1000 to the device (a performance option). "Brctl addif br1 eth0.8" adds "eth0.8" to the "br1" bridge. "Brctl addif ath0.1" adds the 2.4GHz ath0.1 VAP device to the "br1" bridge. "Brctl addif ath1.1" adds the 5GHz ath1.1 VAP to the "br1" bridge.
Again, if you use different VLANs, you should change the vconfig add eth0 line as appropriate.
After you have run those command manually via ssh or the command interface, you should see under "Setup"->"Networking" in the "Current Bridging Table" the br0, br1, and br2 (at least if you setup 2 VLANs) and see the correct devices under each. You should not see the eth0.XXX, ath0.XXX, ath1.XXX under br0, and only see them grouped together under the new bridge devices. You should also see under the VLAN Tagging that eth0 has the new tags.
If this all looks correctly you can save it as a startup script under "Administration"->"Commands" "Save Startup script".
Do not attempt to change the VLANs under the "Setup"->"VLANs" page. Simply ignore that page entirely, it will only cause problems and possibly require you to factory reset.
There are additional settings you need to make if you are using the R9000 as the router. You will want to block access anything from 192.168.<VLAN ID>.XXX going to 192.168.1.XXX. You will also want to block ssh, http, and https from 192.168.<VLAN ID>.XXX from going to 192.168.<VLAN ID>.1 (or whatever you setup the R9000's IP address on the eth0.<VLAN ID> interface). You will need to read up on that from a tutorial.
You will also want to define additional DHCP address spaces for the new VLANs. Again, you can read how to do that on a tutorial for DD-WRT.