At default, presamp will subsitute VCV samples or add on VC samples within the render process, adjusting the consvel and length of the VC based on the consvel within the UST and/or the length that was selected via predit.
The presamp.ini is the configuration file that adds onto or overrides presamp's default settings. It allows one to include romaji/hiragana conversions without needing in-bank aliasing, and other quirky little extras like default vowel endings and whatnot (I'm pretty sure the one in Aiko is the default, Tomki added it in when he split up her wav files). But, as presamp is intended to be an automated process, by default (i.e. without a presamp.ini) it will grab and use the matching VC and - CV depending on the UST phonemes and nothing more. It's based on the standard aliasing method Japanese CVVC tends to use, which is what I originally otoed Aiko with: - CV (beginning of phrase), CV (blending) and V C (with the space between V and C)
If you'd rather throw in manual VC, however, don't fret! Just run predit again to be safe. Presamp knows to not interfere with manual user decisions and you can be free to use manual VC however you like in your tuning, while allowing presamp to do its thing on notes that don't necessarily need any fine-tuning. It prioritizes user-input VC and won't override them. It gets a little trickier when you have a VCV bank aliased with CVVC, though, Halo's had some issues with it being confused between selecting VCV samples and inserting VC. But all Aiko has in VCV style are her vowels and midbreaths ;v;/