I'm no pro but personally I'd say draw it the way whatever you're used to/ feel more comfortable. You may have some sort of 'handiness' when it comes to portraying characters, actions, in which case the panels going from either direction may also enhance certain effects (although I do think this applies more to hard manga copies.)
It could also depend on your target audience (what they're used to reading, which means the genre should be considered too.)
Just some amateur opinions, hope they help a bit ^^;
I agree, draw the way you feel better... If you don't have any restrictions to your work (like japanese manga is commonly read from right to left), you can go either way, so it would depend on who you would be targeting, like Utsune said...
The way characters appear in the panels you might need to be more careful, like, two characters that are in a conversation, it's better to have them "facing" each other even on separate panels... The first one looks to the right, the other to the left, for example... it helps with continuity