I have tried using ganache under fondant a couple of times and had trouble getting the chocolate completely melted without overheating it. I used the tutorial by Three Little Blackbirds the first time and then used the tutorial on here (3 part tutorial) the second time.

Both times I just used chocolate chips (semi-sweet one time and milk chocolate the second time). I wanted to use something readily available so that I didn't have to order it in bulk.

When I used the microwave, I adjusted it to 50% power and a shorter time than in the 3 part video because I didn't want to overheat the chocolate. It took forever to get all of the chips to melt completely. When I did it at full power the chocolate got way too hot, even with a shorter burst of time than in the video.

My question is:

Is it okay to use chocolate chips or do I need to use a different kind of chocolate?

Also, I have a cake tasting coming up where the customer wants to try white chocolate ganache to see if she wants it as the covering for her wedding cake. I have had better success with white chocolate, so I'm not worried about using it as a covering.

My question here is:

She wants a stenciled pattern (houndstooth) around the cake. Can I stencil with royal icing on ganache? I know I can buy houndstooth icing sheets, but I don't like the taste of them and would rather stencil. She would also rather have the stencil instead of the icing sheets.

Thanks in advance!

I don't use the microwave to make ganache. Just don't trust microwaves. I'd rather bring the heavy cream to the right temperature over the stove and then pour over the chocolate. Sure, it's more dirty dishes and takes a bit longer, but it works perfectly every time. Chocolate is something I like to have complete control over because it's so expensive around here. 

I've made ganache with chips.

AYeah, don't melt your chocolate over heat (or in the microwave). Just chop it really fine, scald your cream on the stove, then pour it over the chocolate.

I heat the cream to nearly boiling in the microwave, toss in the chocolate, and let it sit for a minute or two. Then I stir it all together until absolute no chocolate chips/shards/bits remain and it's smooth.

I do not melt the chocolate, I heat the cream.

AI will admit, I have tried the heat the cream method multiple times, but it just does not work for me. I let it sit, I stir and stir, but not all the chocolate melts.

So now I heat the chocolate in the microwave first, then pour the cream, then let sit, then stir. Usually I need to give it another burst in the microwave before I can get the chocolate completely melted. I do it on high, for a minute, and my chocolate seems okay.

A lot of chocolate chips have a waxy coating that is meant to stop them from melting down in cookies, and not clump together in the bag, that makes it hard for the chocolate and cream to emulsify.
I would try bar chocolate or a different brand.
If you really want to use the microwave, you can mix the chocolate and cream together and heat it in the microwave using short blasts of heat, stirring in between, but I wouldn't heat the chocolate alone.

I just recently tried to use chocolate chips for ganache for the first time(Ghirardelli) and it was a complete disaster putting on the cake. Once I put the chocolate on the cake, it started getting hard and lumpy right away and I spent over an hour trying to smooth it.  I would stick with the bar, I've used Ghirardelli and Bakers brand, and have had great results with both.  

What about sticking fondant houndstooth to the ganache? I found this fondant cutout, and you could stick it on using shortening. Of coarse it will take a while to do every houndstooth but will work! Here's one that I found.

https://www.etsy.com/listing/180594241/houndstooth-pattern-cutter-for-fondant?utm_source=google&utm_medium=product_listing_promoted&utm_campaign=housewares_low&gclid=CIj2266s_LwCFS9p7AodsgQAcg

A

I think I had that happen to me too before and it's probably because there was a gap in the cake, like for example one layer was sticking out more than the one underneath it, and chocolate wasn't pushed into that spot good enough making an air bubble. I hope that makes sense! Or maybe it has to do with putting the ganache on right after filling and stacking. I used to do that but now I let the rest for at least a few hours in the fridge for everything to settle. And I used the chocolate chips too trying to save money. I'm not sure if you've heard of Pastry Portal but it's cheaper by the pound to buy chocolate from their site. Dark chocolate is about $4-5 a pound which if you add up even the cheapest you can buy at walmart by the 4 oz bars it comes out to $9/lb (where I live). It comes in 22 lbs though.