BluePhaze I have 9 layers set up per level as a rule. I don't use them all, I just have them there in case I decide to do any strange effects. For the most part I only use 3-4 layers.
As a rule of thumb, my top layer usually contains full screen effects. In this case my 320x240 pixel effect is on this layer. Next one down is typically text/hud. In this games case I dont use 6 at all as far as I remember, in go!go!Maddi! I use it for full screen effects like rain or fog. Layer 5 is the sprite play field. Layer 4 is the map. Layer 3 is multi layered scroll back drop if used. Layer 2 and 1 aren't used here and 0 would be a static background of 320x240 if I need it.
At the start of every layout I have always>system>start of layout>set layer scale 1.25.
Joannesalfa I do most of the graphics right in constuct 2's sprite editor. I'm used to working in that sort of environment from the c64 days of Gary Kitchen's Game Maker and Shoot Em Up Construction kit... That puts a nice age on me ;)
The bigger graphics I partially hand draw and then scan. In the case of the big bosses in this game they are entirely drawn in black and white, scanned taken into photoshop and resized then I go to web export and save as a 4 colour png. Any edits I do in the sprite/graphic editor in construct 2/ classic.
I actually use the sprite editor in CC to adjust the colour and then save and reload in C2. CC has the change color to option in the editor and I really need that feature. So I always have CC and C2 open at the same time when doing gfx. I have a gif of the NES palette loaded in every level layout so I can grab colors quick. And also in CC so I can correct anything I've scanned in quickly.
But yeah for the most part everything I do is pixel by pixel in the sprite editor.
I use that pixel effect because the warp effect for example works at the screen resolution and not the window res. So on my screen everything will look correct until I get to the water section and the water is warping at a way higher res and looks pretty bad against the pixel art.