pokemon emerald uses a hardware clock. The hardware clock is NOT found on the 3in1. There is no way to currently enable RTC (Real Time Clock) features with emerald, via patches to the rom.
You will need to have the M3 GEP (definition of GEP is in my sig). Which does have the hardware clock needed for pokemon emerald.
Your first doubt/question:
The game runs fine regaurdless of the clock. You will not have access to any time based features in the game like daylight/nightime, berries, etc if your running it on the 3in1.
Your second doubt/question:
EEPROM save types being the exception, you can interchange nearly any saves from VBA to GBA Exploader without any modification except for the file naming. GBA Exploader saves all the saves in 1 folder
GBA_SAVE. It is not complicated to drag and drop any saves you need, unless you want to make it more difficult or something.
As for patching roms, that is done on the computer. You can use either the EZ-Flash IV client or the 3in1 tool. These 2 are basically the same thing with different skins, and fixes the save types you can use.
EZ-Flash IV client:
http://filetrip.net/f4753-EZ4-Client-2009-04-03.html
3in1 tool:
http://www.ezflash.cn/zip/3in1tool.zip
Some games require a 2nd or 3rd patch for other things like language, example being mother 3 translation patch, or the light setting patch for boktai. These require other patching tools or comes self contained executables.
AKAIO, stores gba saves like it does with the nds saves, in the same folder as the game. AKAIO gba saves are not directly compatible with gba exploader or VBA, AKAIO puts a header to all gba saves making it incompatible.