those other metals are used to make many of the machines in the game. These machines offer much improvement over using the grindstone for instance.
Want a quick guide?
once you get a vanilla base going: make a grindstone to double ores.
Make an iron chest sometime.. it has the same space as a double wooden chest.
Make some glass when you can.
mine down and get some gold if you can.
harvest some rubber trees.. plant them at your base and chop'n'grow em when you can to ensure you have a decent amount of rubber. smelt rubber to intermediate rubber then again to plastic.
make a dimensional anchor sometime to ensure your machines work while you are offline.
make a steam dynamo and a pulveriser with a hopper to feed it and have it dump into a chest beside it. This can run while you go mine, if you have the dimensional anchor set up in your base.
keep mining.
make an alloy smelter and sag mill.
keep thealloy smelter in alloy mode.
get clay from water areas and combine into blocks then feed them through the sag mill to get silicon.
get the materials to make a 3x3x5tall nuclear reactor (no cooling required).
build a base capacitor bank (enderio mod) and pulse the reactor to feed the cap bank. use the cap bank to feed your machines via red enderio power conduit (needs alloys from alloy smelter)
you will now have ubiquitous power for your machinery.
mine some more, get enough diamonds for a quarry. quarry and filter out cobble and sand and gravel and feed the rest into a pair of gold chests. you will then have to manually mule the ores to your machines.
when you want, go kill some endermen to get ender pearls and make some tesseracts so you can just teleport the materials form the quarry straight back to your machinery in your base.
go to the nether and get nether quartz and glowstone.. careful, the pigmen don't like it when you mine any ore or crystals. glowstone is fine though.
get more pearls and make some deep storages, use em.
build up your enderio armor and weapon.
build up your ME sorting and crafting system.
sometime during all this, keep upgrading your base to look nicer and nicer.
at some point, stop mining with quarries and switch over to using laser drills with bigger reactors and turbines to power them.