I'm not an artist nor am I an animator but I guess it all boils to what you find most comfy to use. For animation / graphics (in general) you could use Art Rage, Adobe Photoshop, Illustrator, Flash etc. You could even use sprite part animation tools such as Spine, Spriter or Anime Studio Pro (tip: Spine animation support should be included in the next update of Visionaire Studio).
Adobe Flash I think sort of works like sprite part animation, as in: you can split animation into different layers, swap them out, morph them & control the animations through key frame events in a time-line (I think).
As for the format... PNG is fine, but I do recommend webp for the final image / animation formats used in game, because...
A. The file sizes are much smaller than PNG which is a lossless image format.
B. It's hard to tell the difference between the PNG & webp formats when you export the webp files out at quality option 10 - highest quality available for lossy option. The next option is lossless, but file size is larger.
C. Because of the smaller file-sizes. the images & animations will load faster, thus the actual requirements to run your game are reduced - good news for people using shitty machines. - Optimization.
P.S: check the wiki. Under documentation is a link to an index page of tutorial links. I linked all of the currently available VS tutorial related videos on it. Also check out the manual under documentation. It is far from complete & I've been too busy to update it. On the manual index page you will find a section that includes links to various tips, one of them is about optimization & the other is about recommended image formats & encoding methods. On the recommended image format page is the link to a really nice freeware batch converter which allows you to convert single, multiple files & entire folders of images to webp & just about any other image format you can think of. I really recommend downloading it.