Magento 1 SQL Queries

Yes you can run direct sql queries within Magento, the best way to do this is to use the read write resource. You can insatiate it with:

    $resource = Mage::getSingleton('core/resource');

    $readConnection = $resource->getConnection('core_read');

    $writeConnection = $resource->getConnection('core_write');

To run a select you can do something like this:

    $readConnection = $resource->getConnection('core_read');

    $query = 'SELECT * FROM ' . $resource->getTableName('catalog/product');

    $results = $readConnection->fetchAll($query);

    /* get the results */
    var_dump($results);

To write something to the database use:

    $resource = Mage::getSingleton('core/resource');

    $writeConnection = $resource->getConnection('core_write');

    $table = $resource->getTableName('catalog/product');

    $query = "UPDATE {$table} SET {item} = '{value}' WHERE entity_id = 'value'";

    $writeConnection->query($query);

Hope this helps out for you.

There is a more proper way to do this to avoid SQL Injections.

$resource = Mage::getSingleton('core/resource');
$write = $resource->getConnection('core_write');
$table = $resource->getTableName('your/model');

You can Create:

$write->insert(
    $table, 
    ['column_1' => 1, 'column_2' => 2]
);

Read:

$select = $write->select()
    ->from(['tbl' => $table], ['entity_id', 'company'])
    ->join(['tbl2' => $table2], 'tbl.entity_id = tbl2.product_id', ['stuff'])
    ->where('name LIKE ?', "%{$name}%")
    ->group('company');
$results = $write->fetchAll($select);

Update:

$write->update(
    $table,
    ['column_1' => 3, 'column_2' => 4],
    ['entity_id = ?' => 123]
);

Delete:

$write->delete(
    $table,
    ['entity_id IN (?)' => [123, 456]]
);

Insert Multiple:

$rows = [
    ['col_1'=>'value1', 'col_2'=>'value2', 'col_3'=>'value3'],
    ['col_1'=>'value3', 'col_2'=>'value4', 'col_3'=>'value5'],
];
$write->insertMultiple($table, $rows);

Insert Update On Duplicate:

$data = [];
$data[] = [
    'sku' => $sku,
    'name' => $name
];
$write->insertOnDuplicate(
    $table,
    $data, // Could also be an array of rows like insertMultiple
    ['name'] // this is the fields that will be updated in case of duplication
);