So do I vac my sand or not?

How fine is Silver Sand? I have heard of it, but it is not available here under that name.

If the tank is well planted, roots spreading all over in the sand do not disturb it deep down. Skim the siphon over the surface enough to pick up the large debris.

If the tank has plants that are growing on driftwood or rock, few or no roots in the sand then I would deep vacuum the sand.

Here is why:
Roots of healthy plants will add oxygen to the substrate. This is very good. Keeps a balance of bacteria that are more of the oxygen types, less of the anaerobic ones.
If there are no roots or very few, or if the plants are not doing well there is less oxygen getting added to the sand.
If the sand is deep, or very fine the water does not circulate through it very well, and low oxygen conditions take over. The bacteria that grow in that sort of substrate can produce toxins that may kill the fish.

Silver sand is extremely fine, rounded sand. The top layer seems to stay quite soft and maluble, but firm up deeper down. It is quite well planted, the only thing growing on the rocks and wood are mosses.

I had only been doing a very light clean of the sand, but will start being more thorough now. While I was reading mixed opinions with only anecdotal reasons behind them I wasn't sure which way to go incase I did somthing wrong. Luckily I have trumpet snails so I don't think my mistake shouldn't be too severe when it comes to gasses, or I hope not atleast. Either way I will do a part water change and sort it tonight.

For doing deeper cleans how would I do that without losing the sand?

I don't know how silver sand compares to PFS, but I usually just vacuum the detritus off the surface of the sand. Weekly I'll go through and gently disturb the deeper portions that my cories and assassin snails don't churn up with a chopstick or bamboo skewer.

I don't own any chopsticks since my wife refuses to use them, and thinks I'm showing off when I do lol, will start getting a fork in there on water change days.

I will have to start being careful with the vacuuming though, one of my ottos was half way up the pipe before I realised, I'm so accustomed to the fish moving out of the way I assumed he had. He seems fine and well though so can't have stressed him too much.