Just for the record, since this question has caused some confusion. Future readers (particularly English learners) may find this useful. The word

impregnate

simply mens "soak". So, if you're an engineer, or you make shoes, you use it constantly, along with words like "weld" or "truss" or "staple".

"OMG, the dye is impregnating the steel plate." "This impregnating machine is crap dude." "How the hell are we going to get the glue to impregnate this weird nylon stuff?"

Here are some impregnating machines,

http://www.menzel-maschinenbau.de/en/products/impregnating-machine-grid-fabric-m2224-05/

http://www.vanwees.nl/products-services/impregnation-machines/ http://www.godfreywing.com/vacuum-impregnation/equipment

Here's some impregnated sleeving (beautiful isn't it?)

http://www.detakta.de/en/glasfibre-sleevings/glassfibre-sleeving-impregnated-with-silicone.html http://www.atkinsandpearce.com/coated-insulation-solutions/suflex/acrylic-sleeving/acryflex-vpi/

Some impregnation substances,

http://www.isomat.eu/Waterproofing-of-walls-by-water-repellent-impregnation.html https://www.youtube.com/watch?v=skST_iPIj1U

Here's some leather impregnation tips,

https://www.youtube.com/watch?v=skST_iPIj1U http://www.schuhdealer.com/shoeblog/schuhe-richtig-impragnieren/

Here's a whole pile of impregnating stuff and impregnated stuff,

http://www.alibaba.com/trade/search?SearchText=impregnating http://www.isve.com/en/impregnation-treatment-and-coating-of-wood-in-autoclave-using-double-vacuum-system

So, impregnate -- soak.

Now, consider the word "impregnable". It has utterly no relationship, in any way, meaningwise or etymologically, to "impregnate". But "impregnable" and "impregnate" (coincidentally) look similar. Further, as the OP points out, various variations of these words are also confusingly similar. (I'm sure you could easily find thousands of examples of people using these words the wrong way, mixing-up the two words: which is an absolutely commonplace phenomenon in English usage.)

Now. I actually do not know what the questions is asking as there is no decisive "question asking" part to the question. But the general tenor of the question seems to be "what's the deal with these two words."

(1) Note that gpr has perfectly explained that there is no, zero, etymological connection.

(2) I suspect that, particularly for any English learners reading in the future, there is some confusion about the word "impregnate"/"soak". I have tried here to take some pains to show the everyday use of the very common normal word "impregnate"-ie-"soak" which has a spectacularly clear meaning (to wit ........... "soak" !) My point with this answer is that hopefully it will make it quite clear that "impregnate"/"soak" has no connection at all to issues of medieval warfare, breaking into castles, etc.

(3) I think the overwhelming takeaway point is that it is utterly common in English that two words "happen to sound or look similar" but in fact have zero connection in any way (meaning, use, or etymology). This is part of the general "English is a spectacular mess" phenomenon of all English spelling and usage. Indeed note that it's a common feature on this site that a, perhaps new English learner, will ask questions about two coincidentally similar words ...... and the answer is nothing more than "oh that's a coincidence, the words are 1000 years apart in etymology and have no connection at all in meaning." This is completely commonplace in English.

(4) A final point is that "sometimes the in- prefix means 'into', and sometimes it means 'negation'." (And additionally im- and in- are simply alternate spellings of the same prefix.) But this observation is so commonplace on this site and ELL that it's barely worth mentioning. (The absolutely obvious joke based on the two meanings of the 'in-' prefix .. "So, is 'duce' the opposite of 'induce' ?! .. hahahahah!" must have been made 100 times on this site; often English learners will ask it for real, not as a joke.)

The confusion with this word is easily solved.
The prefix In, im means not. You are confusing the word pregnant with the word pregnable.
The words are similar but are not the same word.
If you want to say that you can't penetrate a fortress you would say the fortress is impregnable. Or if you could easily break into a fortress then you would say it's pregnable. You can not say impregnatable because that is not a word. You could however say not pregnant but the prefix does not apply to this word.