There are two solutions, a complicated and a simple one. Let's start with the complicated solution: You're recoding both tools in such a way that they don't interfer with each others. This requires knowledge in ASM and C++ and is very impractical to the point of using only one sprite tool and make the sprites compatible is much simpler. The simple solution? Just forget the idea and use either one or the other.
Both tools do the same thing i.e. they both insert sprites, insert their code at the same locations and will interfer each other when used at the same time (this applies to all others tools but also patches in general except for assemblers i.e. you can't have two addmusics or two block tools in the same ROM too). As such, you can only pick between one or the other. However, just because PIXI isn't compatible with romi's Sprite Tools, it is with its sprites. The condition is that they can be assembled with at least xkas (an older assembler, nowadays not really used). For sprites (such as SMB1 Bowser) which are inserted with TRASM (a very ancient assembler, not used at all outside of legacy stuff), you first need to run them through Trashkas
before you can insert them with PIXI. This isn't the whole story since the sprites will only spawn once in the level due to the way how PIXI has changed the sprite load table (i.e. which sprites will reload and which sprite won't).
Okay, my layout looks ugly.