I have a well established base now (1.5.2), and want to start on thaumcraft. I have never played with it before, but have heard warnings about using it in your main base. What is the safe distance, or can I mitigate the problems it causes of I just start a new room in my current facility.
I would actually suggest that you make your thaumcraft lab at your main base. If you make it somewhere far away you will be forced to chunkload the nearby nodes to allow the flux to dissipate. If you do it at your main base, your very presence(or the bases chunkloaders) will help clear the flux.
Setting up lab near a single silverwood tree wont help much either. A silverwood tree contains a very small node, and the deal is that larger nodes will send Vis to nearby nodes that have less vis. All this traffic of vis will cause flux in all your surrounding nodes.
Few of my advices:
Do all the research first before you start on the actual thaumcraft. Two things are almost vital to have at the beginning IMO: Goggles of revealing and Basic flux research(for arcane alembics).
Dont build near an obsidian totem circle. It has a rather large Unstable node in it which will actually produce bad flux. (If you do, you will have to create a larger pure node and merge them to remove the unstable node).
Once you find your main node(the one that covers your lab)(find it with goggles of revealing), build a hollow 3x3x3 cube around it. This will allow wisps to spawn, but will keep them contained. I usually make it out of glass and put in a few fence "posts" so you can kill off the wisps inside with a sword(through the gap between fence and glass). You can also add a melee turtle to kill off some of the wisps should too many spawn.
Once you are set up properly you will want to make your own Pure node for your lab. Pure nodes actually help reduce flux without causing bad stuff(bad stuff(wisps, debuffs etc) remove flux too). Pure nodes are created with silverwood trees. For this you will need a bunch of silverwood saplings(if you have dartcraft use the force mitts on the leaves for increased sapling drops). Now plant a sapling somewhere nearby your lab, but make sure its at least 20 blocks away from any existing nodes. Grow the tree, chop it down, grow a new sapling etc. Each tree will spawn a new small pure node which will merge with the pure node with the first tree. Merging nodes will cause flux, so do it over a period of time, 2-3 saplings at the time. Keep building the node up over time till its the largest in the area. 600+ should do. Having the largest node in the area as main node will prevent/limit borrowing vis from nearby nodes and thereby causing more flux. Flux will more or less then be contained to your main pure node which will get rid of it faster. Having the node contained will prevent wisps from harassing you, and the melee turtle will farm you some wispy essences.
Later you can upgrade your pure node with crystal clusters(just do the fire ones, cheaper to make) and crystal capacitors. Clusters will overcharge your node, making it contain more vis. It will also cause stone in the ground to be converted to shards which will serve as vis batteries. The capacitors will store some excess vis as well once its overcharged and in essence expand your nodes vis storage.
Example of setup: Pure node encased in glass with melee turtle
Right under the node: Crystal clusters and capacitors
Simple melee turtle program: name it startup and it will resume every time you start the game/reloads the chunk, and will empty loot into a chest above it.
http://pastebin.com/nRYFDYNg