Is there an easy process I can go through to show bottlenecks?

Are you trying to find out if you have a bottleneck it in your own network?

Yes basically, would like to see the packetflow and whether I can identify certain areas, whether switch, server, etc

Do you have a dude server setup? You can you build a map of your network and then determine what is using your bandwidth based on utilization. Watching packets is more about troubleshooting problems but if you looking to visualize the traffic try out Hosts3D on sourceforge.

Are you looking for help setting up a dude server?

I've got dude already setup, then I've created seperate maps for various items such as Workstation, Servers, Switches, etc.

Should I create another map? If so how do I then show the traffic, etc

Sounds like you might just need to put connections around between your various maps?
So on your top map is it just a bunch of sub maps, something like one submap for each site? If so you could manually add all the routed links between each site.

The best way to find the traffic you are interested in is put all the routed links in your various maps.

What I did for my routed links is to add a connector between each submap on the main dash, and on each submap I put a link back to the dash showing traffic from the other end of the routed link. So I am collecting routed links on the main dash from the center out and from each submap towards the core. Once you have all your routed links being collected you should be able to determine where there is too much traffic.

HTH,
Lebowski

edit: From your post it sounds like you put different device types on each submap? If you have one submap with all the routers you could organize that map to show all the connections between routers.

I have a map that has the servers defined and ports they connected to on the switch. Is this a good start?

All those links were automatically added from the auto discover process. You might want to turn off auto discover.

With that view you really have no idea where traffic is going. Right click on the map, select add link, place the link between two devices you know are connected to each other. Select the device, mastering type "snmp", change type to match the link speed. Find the interface in the list that is connected to the other device in the interface drop down list.

I put a speed on there so it changes color when there is some traffic. You might delete the other lines if they are not helping you map your network. Also back up your DUDE folder before and after you have made big changes.

Done all that but doesn't seem to show much at all

I would delete all the auto discovered router stuff(links with clouds) and replace it with manually added links. That would give you much more information about traffic around the network...

The broken link are virtual servers but I've not setup the fixed links.

What I now want to do is monitor activity/performance between one server running an MS application but where the SQL database is located on another server. Is this possible with Dude?

Thanks

Not possible if you are talking about monitoring just the SQL traffic. You will need some protocol analysis software for that, there are some free ones out there.

http://www.monitortools.com/traffic/