Once Turkmenistan letter of invitation (LOI) has been issued/ approved you can get the actual transit visa without any difficulties. If you are entering Turkmenistan through one of the land borders you don't actually need to do anything in advance. All you need to do is rock up at the border with some cash in USD (between $60 and $100 depending on nationality), copy of this LOI and your passport. The visa will be stamped into your passport there and then and you'll be able to stay in Turkmenistan for up to 5 days from the date you enter the country.
If, however, you are entering from Azerbaijan (crossing the Caspian sea), you'll need to get the transit visa beforehand. That can be done at the embassies in either Istanbul or Baku in just a couple of days. You will need to tell the embassy that the transit has been pre-approved already and will need to submit your passport, application form (available at the embassy), copy of the LOI, photo and some cash. The visa will then be valid for 5 days according to the dates you request on the application form.
This article has been taken from The Visa Machine's advice pages