Optimising MySQL for Large Queries

Hey guys, I've never been the best at understanding SQL optimisation and I'm hoping I can get some advice here. We have a 6 core VPS with 4GB. The server is dedicated for a single website and it seems to hold up well with traffic so far, " Although when we upload products and information from a CSV via the website (Which we commonly do) the SQL server seems to bottleneck and go down for a few minutes, CPU load is still low but we can't load any pages at all for around 2-3 minutes. When i look at the SQL processes I can see about 30 open connections which are "Sleeping". There are about 2000 lines in our import files on average, We're also running CS-Cart Multi Vendor if that helps. Right now we are running Apache 2.4 and PHP 5.5 I've downloaded the configuration and pasted the contents below. I basically just want to optimize MySQL to handle those large queries and support traffic at the same time. Our traffic isn't that huge right now, We haven't really launched our company yet. Any help appreciated.

"Apache":
  "optmods":
    1: 0
    2: 0
    "Access": 1
    "Actions": 1
    "Alias": 1
    "Asis": 0
    "AuthAnon": 0
    "AuthDB": 0
    "AuthDBM": 0
    "AuthDigest": 0
    "AuthLDAP": 0
    "AuthnAlias": 0
    "AuthnAnon": 0
    "AuthnDBD": 0
    "AuthnDBM": 0
    "AuthnDefault": 1
    "AuthnzLDAP": 0
    "AuthzDBM": 0
    "AuthzHost": 1
    "AuthzOwner": 0
    "Autoindex": 1
    "Bucketeer": 0
    "Cache": 0
    "CaseFilter": 0
    "CaseFilterIn": 0
    "CernMeta": 0
    "CharsetLite": 0
    "DAVFs": 0
    "DAVLock": 0
    "DBD": 0
    "DIR": 1
    "Dav": 0
    "Deflate": 1
    "DiskCache": 0
    "Distcache": 0
    "Dumpio": 0
    "Echo": 0
    "Env": 0
    "Expires": 1
    "ExtFilter": 0
    "Fastcgi": 1
    "FileCache": 0
    "Fileprotect": 1
    "Frontpage": 0
    "Headers": 1
    "Ident": 0
    "Imagemap": 0
    "LDAP": 0
    "LogAgent": 0
    "LogConfig": 1
    "LogForensic": 0
    "LogReferer": 0
    "MPMEvent": 0
    "MPMItk": 0
    "MPMLeader": 0
    "MPMPerchild": 0
    "MPMPrefork": 0
    "MPMThreadpool": 0
    "MPMWorker": 0
    "MemCache": 0
    "Mime": 1
    "MimeMagic": 0
    "MmapStatic": 0
    "Negotiation": 1
    "OptionalFnExport": 0
    "OptionalFnImport": 0
    "OptionalHookExport": 0
    "OptionalHookImport": 0
    "PHPAsUser": 1
    "Proxy": 1
    "RaiseFDSetsize": 0
    "RaiseHardServerLimit": 0
    "Rewrite": 0
    "Setenvif": 1
    "SlowRestartPatch": 0
    "Speling": 0
    "Status": 1
    "SymlinkProtection": 0
    "UniqueId": 1
    "Userdir": 1
    "Usertrack": 0
    "Version": 0
    "VhostAlias": 0
    "Watchdog": 0
  "version": '2_4'
"Cpanel::Easy::EAccelerator": 0
"Cpanel::Easy::IonCubeLoader": 1
"Cpanel::Easy::ModBandwidth": 0
"Cpanel::Easy::ModGzip": 0
"Cpanel::Easy::ModJk": 0
"Cpanel::Easy::ModJk5": 0
"Cpanel::Easy::ModMono": 0
"Cpanel::Easy::ModMono2": 0
"Cpanel::Easy::ModPerl": 0
"Cpanel::Easy::ModQos": 0
"Cpanel::Easy::ModRuid2": 0
"Cpanel::Easy::ModSec": 1
"Cpanel::Easy::PHP5": 1
"Cpanel::Easy::PHP5::3_29": 0
"Cpanel::Easy::PHP5::4_37": 0
"Cpanel::Easy::PHP5::5_21": 1
"Cpanel::Easy::PHP5::Bcmath": 1
"Cpanel::Easy::PHP5::Bz2": 0
"Cpanel::Easy::PHP5::CGI": 0
"Cpanel::Easy::PHP5::Calendar": 1
"Cpanel::Easy::PHP5::Curl": 0
"Cpanel::Easy::PHP5::CurlSSL": 1
"Cpanel::Easy::PHP5::Curlwrappers": 0
"Cpanel::Easy::PHP5::DBX": 0
"Cpanel::Easy::PHP5::Dbase": 0
"Cpanel::Easy::PHP5::DiscardPath": 0
"Cpanel::Easy::PHP5::Enchant": 0
"Cpanel::Easy::PHP5::Exif": 0
"Cpanel::Easy::PHP5::Expat": 0
"Cpanel::Easy::PHP5::FTP": 1
"Cpanel::Easy::PHP5::Fastcgi": 0
"Cpanel::Easy::PHP5::FileInfo": 0
"Cpanel::Easy::PHP5::ForceCGIRedirect": 0
"Cpanel::Easy::PHP5::GD": 1
"Cpanel::Easy::PHP5::Gettext": 1
"Cpanel::Easy::PHP5::HardPHP": 0
"Cpanel::Easy::PHP5::Iconv": 0
"Cpanel::Easy::PHP5::Imap": 1
"Cpanel::Easy::PHP5::Intl": 0
"Cpanel::Easy::PHP5::Java": 0
"Cpanel::Easy::PHP5::MM": 0
"Cpanel::Easy::PHP5::MagicQuotes": 0
"Cpanel::Easy::PHP5::MailHeaders": 0
"Cpanel::Easy::PHP5::Mbregex": 0
"Cpanel::Easy::PHP5::Mbstring": 1
"Cpanel::Easy::PHP5::Mcrypt": 1
"Cpanel::Easy::PHP5::MemoryLimit": 0
"Cpanel::Easy::PHP5::Mhash": 0
"Cpanel::Easy::PHP5::MimeMagic": 0
"Cpanel::Easy::PHP5::Ming": 0
"Cpanel::Easy::PHP5::Mysql": 1
"Cpanel::Easy::PHP5::MysqlOfSystem": 0
"Cpanel::Easy::PHP5::Mysqli": 1
"Cpanel::Easy::PHP5::Openssl": 1
"Cpanel::Easy::PHP5::PDFLib": 0
"Cpanel::Easy::PHP5::PDO": 1
"Cpanel::Easy::PHP5::PDOMySQL": 1
"Cpanel::Easy::PHP5::POSIX": 0
"Cpanel::Easy::PHP5::PathInfoCheck": 0
"Cpanel::Easy::PHP5::Pear": 0
"Cpanel::Easy::PHP5::Pgsql": 1
"Cpanel::Easy::PHP5::Phar": 0
"Cpanel::Easy::PHP5::Pspell": 0
"Cpanel::Easy::PHP5::SNMP": 0
"Cpanel::Easy::PHP5::SOAP": 1
"Cpanel::Easy::PHP5::SQLite3": 0
"Cpanel::Easy::PHP5::SafeMode": 0
"Cpanel::Easy::PHP5::SafePHPCGI": 0
"Cpanel::Easy::PHP5::SilenceDeprecatedPatch": 0
"Cpanel::Easy::PHP5::Sockets": 1
"Cpanel::Easy::PHP5::Swf": 0
"Cpanel::Easy::PHP5::SysTimezone": 1
"Cpanel::Easy::PHP5::TTF": 1
"Cpanel::Easy::PHP5::Tidy": 0
"Cpanel::Easy::PHP5::Versioning": 0
"Cpanel::Easy::PHP5::Wddx": 0
"Cpanel::Easy::PHP5::WithoutIconv": 0
"Cpanel::Easy::PHP5::XSL": 0
"Cpanel::Easy::PHP5::XmlRPC": 0
"Cpanel::Easy::PHP5::XsltSablot": 0
"Cpanel::Easy::PHP5::ZendMultibyte": 0
"Cpanel::Easy::PHP5::Zip": 1
"Cpanel::Easy::PHP5::Zlib": 1
"Cpanel::Easy::PHP5::cPPHPOpts": 1
"Cpanel::Easy::PHPSuHosin": 0
"Cpanel::Easy::SourceGuardian": 0
"Cpanel::Easy::Tomcat::7_0": 0
"Cpanel::Easy::Xcache": 0
"Cpanel::Easy::Zendopt": 0
"_meta":
  "implies":
    "changed": {}

    "circles": {}

  "name": 'Basic (If your previous build has failed, please use this option) (2)'
  "note": 'This configuration includes a very basic set of Apache and PHP options. Key modules include: mod_access, mod_alias, mod_auth, mod_cgi, mod_env, mod_include, mod_rewrite, mod_suexec, mod_userdir mod_suphp. Key PHP options include: Bcmath, Calendar, Sockets, With Mysql, With Zlib. This build will prevent users from reading each others webroots.'

Optimising MySQL for Large Queries

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