With very few exceptions, KSP mods are either parts only (and thus consist only of configuration files) or include plugins written in C# (which work on both Linux and Windows). MechJeb and Protractor specifically I can confidently say work on Linux because I'm using both right now.
All mods - parts or plugins - should be installed to the GameData directory. For example, if KSP were installed in ~/Games/KSP, with MechJeb installed you should have a directory structure that looks something like this:
~/Games/KSP/
...other KSP directories...
GameData/
Squad/
...base game files...
MechJeb2/
Parts/
...MJ part configurations...
Plugins/
...MJ plugin DLL and PluginData files...
Bear in mind that with MechJeb you need to install a MechJeb part on your rocket to see any UI changes. Furthermore, if you're playing in career mode, you'll need to unlock it in the tech tree before it appears.
Yes, you can save a bit of money by not completely filling your fuel tanks.
You can easily verify this in the VAB when you right-click on a fuel tank and watch how the vehicle cost in the lower left corner changes while you increase and decrease the fuel amount.
The prices for one unit of fuel are:
Liquid fuel: 0.8
Oxidizer: 0.16
Solid fuel: 0.6
Monoprop: 1.2
Xenon: 4.0
The price for fuel is already included in the list-prices of all tanks. The 850 funds price tag of a FL-T400 fuel tank, for example, consists of 666.4 funds for the tank itself, 149 funds for the liquid fuel and 30.6 funds for the oxidizer.
However, reducing the fuel amount is really only economical for solid fuel and xenon where fuel-cost is a very large fraction of total part-cost. Liquid fuel, oxidizer and monopropellant are so cheap compared to their tanks that you pay much less when you just substitute the tank with many smaller ones. Three FL-T100 tanks cost (and weight) less than one 75% full FL-T400.
Exception: When you have a manned command pod but no RCS thrusters on the ship, always remember to remove all the monopropellant from it to save both money and mass.
Best Answer
No, if you've purchased the game already, you don't have to purchase it again. If you bought it on Steam, or have transferred your purchase to Steam, your game will be automatically updated.
If you bought the game through kerbalspaceprogram.com, you can download the latest version by logging into the store, and then clicking on the My Account link. Alternatively, you can open the KSP launcher and click the Update button. Enter your account details, and it'll take care of the rest.