Okay, don't feel dumb if you find the immune system confusing. In an effort to unconfuse people I'm posting a simplistic over explanation of under what circumstances your lymph nodes become swollen.
First thing you need to grasp is that there is a network of vessels in your body called the lymphatic system which is connected with the major systems in the body that produce lymphocytes (white blood cells -- spleen, thymus, and bone marrow. It is just as extensive as your blood vessels, except that it transports a clear fluid called 'lymph' which is similar to plasma, but the lymphatic system does not transport red blood cells.
At certain key locations in the body there are lymph nodes which the lymph vessels drain into. The lymph nodes are essentially connective tissue packed tight with lymphocytes (white blood cells) and act as massive filtration systems to capture and destroy invaders. They are also implicated in the process that helps identify invaders and set in motion the body's process for producing antibodies (this is not done directly by the lymph nodes, but rather lymphocytes called T-Cells and B-Cells).
The lymph system, much like the bodies veins, drains towards the trunk of the body where further cleaning and processing of the lymph is done. Which means lymph enterring the lymph node will come from an area more away from the trunk than where the lymph node itself is located. Because the lymph nodes "filter" the lymph, the foreign substances get trapped in the lymph node and travel no further than that lymph node (generally speaking). They have been described a bit like a police station of the immune system.
When a lymph nodes start trapping foreign invaders within itself, it starts to swell in response. This helps trap even more foreign invaders as well as attracts even more white blood cells to the area of primary infection to battle infection.
A number of years ago I had an abcessed molar. The lymph nodes just in front of my left ear swelled up in response (I looked like a chipmunk), but nothing of note went on with the nodes in my neck. Why? Because the nearest lymph nodes for the roots of my molars were those pesky ones in front of my ear and they collected nearly all the bacteria that was trying to spread out from my molars and protected the rest of my body. Fortunately I got myself some good antibiotics and saw a dentist and everything went back to normal.
So if you have a throat infection or head cold, the nodes in your neck will get enlarged, but not the ones in your groin or armpits. Conversely, because and STD infection (herpes, gonorhea, etc.) is focused in your genital region, the nodes in your groin will get enlarged, but not your neck. There are some infections that will lead to generalized swelling of your lymph nodes, but herpes is not typically one of these.
If during a primary herpes OB you experienced swelling of lymph nodes in both your neck and groin, the most likely explanation is that that with your immune function down you contracted some sort of cold/flu/throat infection on top of the herpes infection. Because we are constantly exchanging air through our mouth and nose, we are often exposed to pathogens in this area, therefore, it is a pretty common thing to have the neck lymph nodes somewhat inflamed because of this ... they are very busy a lot of the time whether you have other symptoms or not.
I hope this is helpful.
Hoe eet jy 'n olifant? Bietjie vir bietjie.
(Translation from Afrikaans: How do you eat an elephant? Bit by bit.)