I still don't know what rom you're even editing...
Nevertheless, you should probably use some game-specific editor which lets you edit insert new sprites and replace the original ones with those. It's really not worth it trying to edit the sprites "by hand". After all, they're most likely compressed which means that the only way to edit them to make them look good is to actually make an image and insert it to the rom file with a tool that compresses the sprite while at it (so that it's displayed properly in the game where it uncompresses the sprite before it loads it into the screen).
You're talking about scripting in gen III right? You can script with both and even if hex if you like. It really makes no difference to use all kinds of tools for the job.
In other words, let's say you open script code from address 0x12345678 with pksv, write some script there and compile it. This makes pksv write the script you edited in byte code into the rom.
If you want to edit the same script with xse later on, it will decompile byte code starting at 0x12345678, show it as "xse script", and once you click compile, it writes the script as byte code again. The same actual byte codes in pksv and xse are written differently in form of textual language, but it doens't matter if you mix the tools up.
Not sure if that makes any sense or not, but when you understand, what precisely happens when you click (de)compile button with a script editor you use, it's straightforward to see it doesn't matter if you use both of them for editing. You shouldn't have the same rom file opened in both editors at the same time though.
Dark Rising, Dark Rising 2, Dark Rising Ordered Destroyed, Korosu, Giratina Strikes Back, Ruby Destiny: Reign of Legends, Ruby Destiny: Rescue Rangers, Ruby Destiny: Life of Guardians, Light Platinum, Dark Rising Worlds Collide (final version January 2017), Theta Emerald EX, CAWPS, Outlaw, My Ass, Flora Sky, Sigma Emerald, Kanto Black, Yet Another Fire Red Hack, Nameless Fire Red Project, and I forgot.....
Just like you said on his profile; he has logged on today. I was just wondering if he's ever gonna come back, he's gonna reply to all of them. Poor guy can't catch a break. His fans don't understand what kind of condition Aethestode is in, and rather than praying him a good life, decided to complain to Aethestode and force him to finish his hack.